Analysis of zinc binding sites in protein crystal structures
Open accessAbstract
The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H‐bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi‐zinc sites. We find that H‐bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec‐His‐Zn motif. Analysis of the stereochemistry shows that carboxyl elec‐His‐Zn motifs are geometrically rigid, while water elec‐His‐Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.
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An electrostatic model based on the filled valence orbital of Zn2+ cannot explain why histidine and cysteine are more common zinc-coordinating residues than the more electronegative carboxylates of glutamate and aspartate.
“Also, an electrostatic model based on the filled valence orbital of the Zn2+ ion fails to explain the prevalence of histidine and cysteine over the more electronegative carboxylate groups of glutamate and aspartate as the most frequent zinc coordinating residues.14−17”
From AutoDock4<sub>Zn</sub>: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins (2014) · cites this paper as [16]
Section 2 (page unavailable) reports the frequency of zinc-coordinating residues in Figure 1, and the coordination-geometry discussion says histidine predominates in mono-zinc sites. Our copy does not establish the claimed overall comparison for both histidine and cysteine against glutamate and aspartate, or say that a filled-valence-orbital electrostatic model fails to explain it. (LLM, conf=0.76)
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Cites
(1999) · Choice Reviews Online · doi:10.5860/choice.37-0940 · Cited by 14,314 · see citing works
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,582 · see citing works
Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80134-2 · Cited by 6,412 · see citing works
The Galvanization of Biology: A Growing Appreciation for the Roles of Zinc
Berg, J. M., & Shi, Y. (1996) · Science · doi:10.1126/science.271.5252.1081 · Cited by 1,930 · see citing works
The PROSITE database, its status in 1995
Bairoch, A., Bucher, P., & Hofmann, K. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.189 · Cited by 1,929 · see citing works
Zinc coordination, function, and structure of zinc enzymes and other proteins
Vallée, B. L., & Auld, D. S. (1990) · Biochemistry · doi:10.1021/bi00476a001 · Cited by 1,784 · see citing works
Recent Advances in Zinc Enzymology
Lipscomb, W. N., & Sträter, N. (1996) · Chemical Reviews · doi:10.1021/cr950042j · Cited by 1,367 · see citing works
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., MOTHERWELL, W. D. S., et al. (1979) · Acta Crystallographica Section B · doi:10.1107/s0567740879009249 · Cited by 1,167 · see citing works
ZINC PROTEINS: Enzymes, Storage Proteins, Transcription Factors, and Replication Proteins
Coleman, J. E. (1992) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.61.070192.004341 · Cited by 980 · see citing works
Reaction mechanism of alkaline phosphatase based on crystal structures
Kim, E. E., & Wyckoff, H. W. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90724-k · Cited by 958 · see citing works
Determination and analysis of the 2 Å structure of copper, zinc superoxide dismutase
Tainer, J. A., Getzoff, E. D., Beem, K. M., Richardson, J. S., & Richardson, D. C. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90174-7 · Cited by 948 · see citing works
The catalytic mechanism of carbonic anhydrase: implications of a rate-limiting protolysis of water
Silverman, D. N., & Lindskog, S. F. (1988) · Accounts of Chemical Research · doi:10.1021/ar00145a005 · Cited by 748 · see citing works
Stöcker, W., Grams, F., Reinemer, P., Bode, W., Baumann, U., Gomis‐Rüth, F. X., & McKay, D. (1995) · Protein Science · doi:10.1002/pro.5560040502 · Cited by 725 · see citing works
The structure of 2Zn pig insulin crystals at 1.5 Å resolution
Baker, E. N., Blundell, T. L., Cutfield, J. F., Dodson, E. J., Dodson, G. G., Hodgkin, D. M. C., Hubbard, R. E., Isaacs, N. W., Reynolds, C. D., Sakabe, K., et al. (1988) · Philosophical transactions of the Royal Society of London. Series B, Biological sciences · doi:10.1098/rstb.1988.0058 · Cited by 666 · see citing works
Zhang, G., Kazanietz, M. G., Blumberg, P. M., & Hurley, J. H. (1995) · Cell · doi:10.1016/0092-8674(95)90011-x · Cited by 653 · see citing works
A structural taxonomy of DNA-binding domains
Harrison, S. C. (1991) · Nature · doi:10.1038/353715a0 · Cited by 609 · see citing works
Christianson, D. W., & Lipscomb, W. N. (1989) · Accounts of Chemical Research · doi:10.1021/ar00158a003 · Cited by 606 · see citing works
Calcium Ion Coordination: A Comparison with That of Beryllium, Magnesium, and Zinc
Katz, A. K., GLUSKER, J. P., Beebe, S., & Bock, C. W. (1996) · Journal of the American Chemical Society · doi:10.1021/ja953943i · Cited by 546 · see citing works
Refined structure of human carbonic anhydrase II at 2.0 Å resolution
Sauer-Eriksson, A. E., Jones, T. A., & Liljas, A. (1988) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340040406 · Cited by 545 · see citing works
Baumann, U., Wu, S., Flaherty, K. M., & McKay, D. (1993) · The EMBO Journal · doi:10.1002/j.1460-2075.1993.tb06009.x · Cited by 473 · see citing works
Structural Aspects of Metal Liganding to Functional Groups in Proteins
GLUSKER, J. P. (1991) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60534-3 · Cited by 452 · see citing works
Structure of thermolysin refined at 1.6 Å resolution
Holmes, M., & Matthews, B. W. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90319-9 · Cited by 439 · see citing works
McGregor, M. J., Islam, S. A., & Sternberg, M. J. E. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90314-7 · Cited by 423 · see citing works
Elrod-Erickson, M., Rould, M. A., Nekludova, L., & Pabo, C. O. (1996) · Structure · doi:10.1016/s0969-2126(96)00125-6 · Cited by 421 · see citing works
Refined crystal structure of carboxypeptidase a at 1·54 Å resolution
Rees, D. C., Lewis, M., & Lipscomb, W. N. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80024-2 · Cited by 401 · see citing works
Christianson, D. W. (1991) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60538-0 · Cited by 374 · see citing works
Crystal structure of the wide-spectrum binuclear zinc β-lactamase from Bacteroides fragilis
Concha, N. O., Rasmussen, B. A., Bush, K., & Herzberg, O. (1996) · Structure · doi:10.1016/s0969-2126(96)00089-5 · Cited by 359 · see citing works
Bode, W., Reinemer, P., Huber, R., Kleine, T., Schnierer, S., & Tschesche, H. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06378.x · Cited by 339 · see citing works
Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases
Bode, W., Gomis‐Rüth, F. X., Huber, R., Zwilling, R., & Stöcker, W. (1992) · Nature · doi:10.1038/358164a0 · Cited by 333 · see citing works
Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer
Derewenda, U., Derewenda, Z. S., Dodson, E. J., Dodson, G. G., Reynolds, C. D., Smith, G. D., Sparks, C. A., & Swenson, D. C. (1989) · Nature · doi:10.1038/338594a0 · Cited by 319 · see citing works
Burmeister, W. P., Cottaz, S., Driguez, H., Iori, R., Palmieri, S., & Henrissat, B. (1997) · Structure · doi:10.1016/s0969-2126(97)00221-9 · Cited by 288 · see citing works
X-ray analysis (1. 4-Å resolution) of avian pancreatic polypeptide: Small globular protein hormone
Blundell, T. L., Pitts, J. E., Tickle, I. J., Wood, S., & Wu, C.-W. (1981) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.78.7.4175 · Cited by 282 · see citing works
Crystal structures of matrilysin-inhibitor complexes
Browner, M. F., Smith, W. W., & Castelhano, A. L. (1995) · Biochemistry · doi:10.1021/bi00020a004 · Cited by 263 · see citing works
Structural similarity between TAFs and the heterotetrameric core of the histone octamer
Xie, X., Kokubo, T., Cohen, S. L., Mirza, U. A., Hoffmann, A., Chait, B. T., Roeder, R. G., Nakatani, Y., & Burley, S. K. (1996) · Nature · doi:10.1038/380316a0 · Cited by 261 · see citing works
Chevrier, B., Schalk, C., d'Orchymont, H., Rondeau, J., Moras, D., & Tarnus, C. (1994) · Structure · doi:10.1016/s0969-2126(00)00030-7 · Cited by 244 · see citing works
Construction of new ligand binding sites in proteins of known structure
Hellinga, H. W., & Richards, F. M. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90510-d · Cited by 238 · see citing works
A new force field for modeling metalloproteins
Vedani, A., & Huhta, D. W. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00168a021 · Cited by 237 · see citing works
New perspective on zinc biochemistry: Cocatalytic sites in multi-zinc enzymes
Vallée, B. L., & Auld, D. S. (1993) · Biochemistry · doi:10.1021/bi00077a001 · Cited by 236 · see citing works
LESSONS FROM ZINC-BINDING PEPTIDES
Berg, J. M., & Godwin, H. A. (1997) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.26.1.357 · Cited by 227 · see citing works
Hydration of Zinc Ions: A Comparison with Magnesium and Beryllium Ions
Bock, C. W., Katz, A. K., & GLUSKER, J. P. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00118a012 · Cited by 216 · see citing works
Holden, H. M., Tronrud, D. E., Monzingo, A. F., Weaver, L. H., & Matthews, B. W. (1987) · Biochemistry · doi:10.1021/bi00400a008 · Cited by 203 · see citing works
Three-dimensional structure of the elastase of Pseudomonas aeruginosa at 1.5-A resolution.
THAYER, M. M., Flaherty, K. M., & McKay, D. B. (1991) · PubMed · doi:10.2210/pdb1ezm/pdb · Cited by 198 · see citing works
Hall, T. M. T., Porter, J. A., Beachy, P. A., & Leahy, D. J. (1995) · Nature · doi:10.1038/378212a0 · Cited by 198 · see citing works
Three-dimensional structure of the elastase of Pseudomonas aeruginosa at 1.5-A resolution.
THAYER, M. M., Flaherty, K. M., & McKay, D. B. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)49927-9 · Cited by 190 · see citing works
1.56 Å structure of mature truncated human fibroblast collagenase
Spurlino, J. C., Smallwood, A. M., Carlton, D. D., Banks, T. M., Vavra, K. J., Johnson, J. S., Cook, E. R., Falvo, J., Wahl, R. C., Pulvino, T. A., et al. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340190203 · Cited by 184 · see citing works
Kiefer, L. L., Paterno, S. A., & Fierke, C. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00131a004 · Cited by 181 · see citing works
Grams, F., Reinemer, P., Powers, J. C., Kleine, T., Pieper, M. P., Tschesche, H., Huber, R., & Bode, W. (1995) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1995.tb20329.x · Cited by 180 · see citing works
Structures of Horse Liver Alcohol Dehydrogenase Complexed with NAD+ and Substituted Benzyl Alcohols
Ramaswamy, S., Eklund, H., & Plapp, B. V. (1994) · Biochemistry · doi:10.1021/bi00183a028 · Cited by 177 · see citing works
Crystal Structure of the 50 Kda Metallo Protease from Serratia marcescens
Baumann, U. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1576 · Cited by 175 · see citing works
Sträter, N., & Lipscomb, W. N. (1995) · Biochemistry · doi:10.1021/bi00045a021 · Cited by 172 · see citing works
Carboxylate-histidine-zinc interactions in protein structure and function
Christianson, D. W., & Alexander, R. (1989) · Journal of the American Chemical Society · doi:10.1021/ja00198a065 · Cited by 165 · see citing works
Crystal Structures of Recombinant 19-kDa Human Fibroblast Collagenase Complexed to Itself
Lovejoy, B., Hassell, A. M., Luther, M., Weigl, D., & Jordan, S. R. (1994) · Biochemistry · doi:10.1021/bi00193a006 · Cited by 156 · see citing works
The NMR structure of the inhibited catalytic domain of human stromelysin–1
Gooley, P. R., O’Connell, J. F., Marcy, A. I., Cuca, G. C., Salowe, S. P., Bush, B. L., Hermes, J. D., Esser, C. K., Hagmann, W. K., Springer, J. P., et al. (1994) · Nature Structural & Molecular Biology · doi:10.1038/nsb0294-111 · Cited by 154 · see citing works
Geometry of interaction of metal ions with histidine residues in protein structures
Chakrabarti, P. (1990) · Protein Engineering Design and Selection · doi:10.1093/protein/4.1.57 · Cited by 152 · see citing works
Dauter, Z., Wilson, K. S., Sieker, L. C., Moulis, J., & Meyer, J. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.17.8836 · Cited by 152 · see citing works
Protein design: novel metal-binding sites
Regan, L. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89044-1 · Cited by 148 · see citing works
Structural stability in the 4-zinc human insulin hexamer.
Smith, G. D., Swenson, D. C., Dodson, E. J., Dodson, G. G., & Reynolds, C. D. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.22.7093 · Cited by 142 · see citing works
Inhibition and catalysis of carbonic anhydrase
Liljas, A., HÅKANSSON, K., JONSSON, B. H., & Xue, Y. (1994) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1994.tb19909.x · Cited by 140 · see citing works
Sträter, N., & Lipscomb, W. N. (1995) · Biochemistry · doi:10.1021/bi00028a033 · Cited by 139 · see citing works
Batimastat, a potent matrix mealloproteinase inhibitor, exhibits an unexpected mode of binding.
Botos, I., Scapozza, L., Zhang, D., Liotta, L. A., & Meyer, E. F. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.7.2749 · Cited by 138 · see citing works
Zhang, D., Botos, I., Gomis‐Rüth, F. X., Doll, R. J., Blood, C. H., Njoroge, F. G., Fox, J. W., Bode, W., & MEYER, E. F. J. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.18.8447 · Cited by 134 · see citing works
Holland, D. R., Tronrud, D. E., Pley, H. W., Flaherty, K. M., Stark, W., Jansonius, J. N., McKay, D., & Matthews, B. W. (1992) · Biochemistry · doi:10.1021/bi00161a008 · Cited by 131 · see citing works
Papageorgiou, A. C., Acharya, K. R., Shapiro, R., Passalacqua, E. F., Brehm, R. D., & Tranter, H. S. (1995) · Structure · doi:10.1016/s0969-2126(01)00212-x · Cited by 123 · see citing works
Crystal structure of tRNA‐guanine transglycosylase: RNA modification by base exchange.
Romier, C., Reuter, K., Suck, D., & Ficner, R. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00646.x · Cited by 116 · see citing works
The X-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 Å resolution
Cleasby, A., Wonacott, A. J., Skarzynski, T. J., Hubbard, R. E., Davies, G. J., Proudfoot, A. E. I., Bernard, A. R., Payton, M. A., & Wells, T. N. C. (1996) · Nature Structural Biology · doi:10.1038/nsb0596-470 · Cited by 115 · see citing works
X-ray crystallographic studies of engineered hydrogen bond networks in a protein-zinc binding site
Lesburg, C. A., & Christianson, D. W. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00131a005 · Cited by 106 · see citing works
Alpha-lactalbumin possesses a distinct zinc binding site.
Ren, J., Stuart, D. I., & Acharya, K. R. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)36512-3 · Cited by 104 · see citing works
Perutz, M. F., Gronenborn, A. M., Clore, G. M., Fogg, J. H., & Shih, D. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90016-6 · Cited by 103 · see citing works
Similarities in active center geometries of zinc-containing enzymes, proteases and dehydrogenases
Argos, P., Garavito, R. M., Eventoff, W., Rossmann, M. G., & Brändén, C.-I. (1978) · Journal of Molecular Biology · doi:10.1016/0022-2836(78)90356-x · Cited by 103 · see citing works
Structure of cobalt carbonic anhydrase complexed with bicarbonate
Håkansson, K., & Wehnert, A. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90327-g · Cited by 90 · see citing works
Structures of Three Human β Alcohol Dehydrogenase Variants
Hurley, T. D., BOSRON, W. F., Stone, C. L., & Amzel, L. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1382 · Cited by 89 · see citing works
The prediction and characterization of metal binding sites in proteins
Gregory, D. S., Martin, A. C. R., Cheetham, J. C., & Rees, A. R. (1993) · Protein Engineering Design and Selection · doi:10.1093/protein/6.1.29 · Cited by 87 · see citing works
The structure of neutral protease from Bacillus cereus at 0.2‐nm resolution
Stark, W., Pauptit, R. A., Wilson, K. S., & Jansonius, J. N. (1992) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1992.tb17109.x · Cited by 78 · see citing works
X-Ray Crystallographic Studies of Engineered Hydrogen Bond Networks in a Protein-Zinc Binding Site
Lesburg, C. A., & Christianson, D. W. (1995) · Journal of the American Chemical Society · doi:10.2210/pdb1cng/pdb · Cited by 76 · see citing works
Lippard, S. J., Burger, A. R., Uǧurbil, K., Pantoliano, M. W., & Valentine, J. S. (1977) · Biochemistry · doi:10.1021/bi00625a017 · Cited by 71 · see citing works
Sequential Structural Changes upon Zinc and Calcium Binding to Metal-free Concanavalin A
Bouckaert, J. M. J., Poortmans, F., Wyns, L., & Loris, R. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.27.16144 · Cited by 69 · see citing works
Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides,
Cho, H., Ramaswamy, S., & Plapp, B. V. (1997) · Biochemistry · doi:10.1021/bi9624604 · Cited by 53 · see citing works
Ramaswamy, S., Ahmad, M. E., Danielsson, O., Jörnvall, H., & Eklund, H. (1996) · Protein Science · doi:10.1002/pro.5560050410 · Cited by 51 · see citing works
The catalytic mechanism of carbonic anhydrase
Silverman, D. N. (1991) · Canadian Journal of Botany · doi:10.1139/b91-137 · Cited by 51 · see citing works
Inhibition and catalysis of carbonic anhydrase
Liljas, A., Håkansson, K., Jonsson, B. H., & Xue, Y. (1994) · Springer eBooks · doi:10.1007/978-3-642-79502-2_1 · Cited by 50 · see citing works
Carbonic anhydrase and the role of orientation in catalysis
Lindskog, S. F., & Liljas, A. (1993) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(93)90156-f · Cited by 47 · see citing works
Djinović‐Carugo, K., Battistoni, A., Carrı̀, M. T., Polticelli, F., Desideri, A., Rotilio, G., Coda, A., Wilson, K. S., & Bolognesi, M. (1996) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444995007608 · Cited by 43 · see citing works
Carver, J. A., & Bradbury, J. (1984) · Biochemistry · doi:10.1021/bi00316a012 · Cited by 43 · see citing works
Structure of the Zinc Endoprotease from Streptomyces caespitosus
Kurisu, G., Kinoshita, T., Sugimoto, A., Nagara, A., Kai, Y., KASAI, N., & Harada, S. (1997) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a021587 · Cited by 43 · see citing works
Binding site‐shaped repeated sequences of bacterial wall peptidoglycan hydrolases
Ghuysen, J., Lamotte‐Brasseur, J., Joris, B., & Shockman, G. D. (1994) · FEBS Letters · doi:10.1016/0014-5793(94)80577-6 · Cited by 42 · see citing works
Lebioda, L., & Stec, B. (1989) · Journal of the American Chemical Society · doi:10.1021/ja00204a030 · Cited by 41 · see citing works
Lebioda, L., & Stec, B. (1989) · Journal of the American Chemical Society · doi:10.2210/pdb4enl/pdb · Cited by 31 · see citing works
Christianson, D. W., & Alexander, R. (1990) · Nature · doi:10.1038/346225b0 · Cited by 30 · see citing works
Dreyer, M., & Schulz, G. E. (1996) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444996009146 · Cited by 29 · see citing works
Metalloprotein Crystallography
Armstrong, W. H. (1988) · ACS symposium series · doi:10.1021/bk-1988-0372.ch001 · Cited by 11 · see citing works
Ab, C., Shimoni, L., Carrell, C. J., Bock, C. W., Murray‐Rust, P., & GLUSKER, J. P. (1993) · PubMed · Cited by 7 · see citing works
Metalloprotein Crystallography Survey of Recent Results and Relationships to Model Studies
Armstrong, W. H. (1988) · Cited by 6 · see citing works
Structural analysis ofSerratiaprotease
Hamada, K., Hiramatsu, H., Fujiwara, T., Katsuya, Y., Hata, Y., Matsuura, Y., & Katsube, Y. (1993) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s010876737809707x · Cited by 4 · see citing works
Ramanadham, M., Jakkal, V. S., & Chidambaram, R. (1993) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767378095628 · Cited by 3 · see citing works
Flagged first, then by citations
Research works printed but not linked: 4
- [33]33. FA, Wilkinson G. 1988. Advanced inorgunic chemistry. New York: Wiley.
- [38]38. Eriksson AE, Jones TA, Lilsjas A. 1986. Zinc enzymes. In: Bertini I, Luchinat C, Maret W, Zeppezauer M, eds. Progress in inorganic biochemistry and biophysics. Vol. 1. Cambridge, MA: Burkhauser. pp 317-328.
- [82]82. Wallace A. 1996. The role of His in metal binding sites. Chapter 7 [PhD thesis]. Am Chem Soc 112:4759-4767.
- [88]88. 1469896x, 1998, 8, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/pro.5560070805, Wiley Online Library on [15/08/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
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Sorted by citations
Synthetic Analogues Relevant to the Structure and Function of Zinc Enzymes
Parkin, G. (2004) · Chemical Reviews · doi:10.1021/cr0206263 · Cited by 935 · see citing works
Structural classification of zinc fingers: SURVEY AND SUMMARY
Krishna, S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg161 · Cited by 913 · see citing works
A cryptic protease couples deubiquitination and degradation by the proteasome
Yao, T., & Cohen, R. E. (2002) · Nature · doi:10.1038/nature01071 · Cited by 727 · see citing works
“Rather, the identities of the critical residues suggest that Rpn11 is a Zn 2p -dependent metalloproteas”
BackgroundCurtain, C. C., Ali, F. E. A., Volitakis, I., Cherny, R. A., Norton, R. S., Beyreuther, K. T., Barrow, C. J., Masters, C. L., Bush, A. I., & Barnham, K. J. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m100175200 · Cited by 653 · see citing works
AlphaFill: enriching AlphaFold models with ligands and cofactors
Hekkelman, M. L., de Vries, I., Joosten, R. P., & Perrakis, A. (2023) · Nature Methods · doi:10.1038/s41592-022-01685-y · Cited by 511 · see citing works
“Typically, it is involved in catalysis or in maintaining structural integrity 19 .”
BackgroundStructure of the zinc-binding domain of an essential component of the hepatitis C virus replicase
Tellinghuisen, T. L., Marcotrigiano, J., & Rice, C. M. (2005) · Nature · doi:10.1038/nature03580 · Cited by 485 · see citing works
Principles Governing Mg, Ca, and Zn Binding and Selectivity in Proteins
Dudev, T., & Lim, C. (2003) · Chemical Reviews · doi:10.1021/cr020467n · Cited by 463 · see citing works
Protein Design: Toward Functional Metalloenzymes
Yu, F., Cangelosi, V. M., Zastrow, M. L., Tegoni, M., Plegaria, J. S., Tebo, A. G., Mocny, C. S., Ruckthong, L., Qayyum, H., & Pecoraro, V. L. (2014) · Chemical Reviews · doi:10.1021/cr400458x · Cited by 442 · see citing works
The Function of Zinc Metallothionein: A Link between Cellular Zinc and Redox State
Maret, W. (2000) · Journal of Nutrition · doi:10.1093/jn/130.5.1455s · Cited by 417 · see citing works
Mony, L., Kew, J. N. C., Gunthorpe, M. J., & Paoletti, P. (2009) · British Journal of Pharmacology · doi:10.1111/j.1476-5381.2009.00304.x · Cited by 404 · see citing works
“, 2005), and bearing side chains commonly found in zinc-binding sites (Alberts et al., 1998).”
BackgroundThe NS5A Protein of Hepatitis C Virus Is a Zinc Metalloprotein
Tellinghuisen, T. L., Marcotrigiano, J., Gorbalenya, A. E., & Rice, C. M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m407787200 · Cited by 356 · see citing works
Differential Metal Selectivity and Gene Expression of Two Zinc Transporters from Rice
Ramesh, S. A., Shin, R., Eide, D. J., & Schachtman, D. P. (2003) · PLANT PHYSIOLOGY · doi:10.1104/pp.103.026815 · Cited by 350 · see citing works
Santos-Martins, D., Forli, S., Ramos, M. J., & Olson, A. J. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500209e · Cited by 318 · see citing works
Zinc Coordination Spheres in Protein Structures
Laitaoja, M., Valjakka, J., & Jänis, J. (2013) · Inorganic Chemistry · doi:10.1021/ic401072d · Cited by 263 · see citing works
Role of Zinc in Human Islet Amyloid Polypeptide Aggregation
Brender, J., Hartman, K. L., Nanga, R. P. R., Popovych, N., de la Salud‐Bea, R., Vivekanandan, S., Marsh, E. N. G., & Ramamoorthy, A. (2010) · Journal of the American Chemical Society · doi:10.1021/ja1007867 · Cited by 238 · see citing works
van Santen, Y., BENEN, J. A. E., Schröter, K.-H., Kalk, K. H., Armand, S., Visser, J., & Dijkstra, B. W. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.43.30474 · Cited by 240 · see citing works
Tetrahedral vs Octahedral Zinc Complexes with Ligands of Biological Interest: A DFT/CDM Study
Dudev, T., & Lim, C. (2000) · Journal of the American Chemical Society · doi:10.1021/ja0010296 · Cited by 232 · see citing works
van den Elsen, J. M. H., Kuntz, D. A., & Rose, D. R. (2001) · The EMBO Journal · doi:10.1093/emboj/20.12.3008 · Cited by 221 · see citing works
Structural Basis of Ubiquitin Recognition by the Deubiquitinating Protease USP2
Renatus, M., Gil-Parrado, S., D'Arcy, A., Eidhoff, U., Gerhartz, B., Hassiepen, U., Pierrat, B., Riedl, R., Vinzenz, D., Worpenberg, S., et al. (2006) · Structure · doi:10.1016/j.str.2006.06.012 · Cited by 212 · see citing works
“(Alberts et al., 1998).”
Zinc and mechanical prowess in the jaws of Nereis , a marine worm
Lichtenegger, H. C., Schöberl, T., Ruokolainen, J., Cross, J. O., Heald, S. M., Birkedal, H., Waite, J. H., & Stucky, G. D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1632658100 · Cited by 214 · see citing works
Guy, C. S., Mitrea, D. M., Chou, P.-C., Temirov, J. P., Vignali, K. M., Liu, X., Zhang, H., Kriwacki, R. W., Bruchez, M. P., Watkins, S. C., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01176-4 · Cited by 214 · see citing works
Dudev, T., Lin, Dudev, M., & Lim, C. (2003) · Journal of the American Chemical Society · doi:10.1021/ja0209722 · Cited by 205 · see citing works
Bae, E., & Phillips, G. N. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m401865200 · Cited by 196 · see citing works
Crystal Structure of a Thermophilic Cytochrome P450 from the Archaeon Sulfolobus solfataricus
Yano, J. K., Koo, L. S., Schuller, D. J., Li, H., de Montellano, P. R. O., & Poulos, T. L. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m004281200 · Cited by 191 · see citing works
Brown, B. L., Grigoriu, S., Kim, Y., Arruda, J. M., Davenport, A., Wood, T. K., Peti, W., & Page, R. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000706 · Cited by 190 · see citing works
“The zinc, which serves a structural and not catalytic role [41,42], is coordinated by four cysteines (Cys3, Cys6, Cys37, Cys40) with an average sulfur-zinc distance of 2.”
BackgroundCameron, A. D., Ridderström, M., Olin, B., & Mannervik, B. (1999) · Structure · doi:10.1016/s0969-2126(99)80174-9 · Cited by 184 · see citing works
“higher coordination number when present in catalytic sites [24], particularly when part of a zinc cluster [25]; for example, both leucine aminopeptidase [26] and purple acid phosphatase [27] contain an octahedrally coordinated zinc ion as part of a binuclear metal cluster.”
BackgroundZinc hydrolases: the mechanisms of zinc-dependent deacetylases
Hernick, M., & Fierke, C. A. (2004) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2004.08.006 · Cited by 178 · see citing works
A Zinc-binding Region in Vif Binds Cul5 and Determines Cullin Selection
Mehle, A., Thomas, E. R., Rajendran, K. S., & Gabuzda, D. H. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m602413200 · Cited by 175 · see citing works
Metalloregulatory proteins: Metal selectivity and allosteric switching
Reyes-Caballero, H., Campanello, G. C., & Giedroc, D. P. (2011) · Biophysical Chemistry · doi:10.1016/j.bpc.2011.03.010 · Cited by 169 · see citing works
New perspectives of zinc coordination environments in proteins
Maret, W. (2011) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2011.11.018 · Cited by 167 · see citing works
Atomic Proximity between S4 Segment and Pore Domain in Shaker Potassium Channels
Lainé, M., Lin, M., Bannister, J. P., Silverman, W. R., Mock, A. F., Roux, B., & Papazian, D. M. (2003) · Neuron · doi:10.1016/s0896-6273(03)00468-9 · Cited by 165 · see citing works
Coordination and catalysis of Zn 2+ in epoxy-based vitrimers
Demongeot, A., Mougnier, S., Okada, S., Soulié‐Ziakovic, C., & Tournilhac, F. (2016) · Polymer Chemistry · doi:10.1039/c6py00752j · Cited by 165 · see citing works
Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone.
Hasemann, C. A., Lee, Y.-H., Deka, R. K., Norgard, M. V., & Radolf, J. D. (1999) · Nature Structural Biology · doi:10.1038/10677 · Cited by 164 · see citing works
Pérez‐Sala, D., Oeste, C. L., Martínez, A. E., Carrasco, M., Garzón, B. S., & Cañada, F. J. (2015) · Nature Communications · doi:10.1038/ncomms8287 · Cited by 161 · see citing works
Zn2+-binding and molecular determinants of tetramerization in voltage-gated K+ channels.
Choe, S., Bixby, K. A., Nanao, M., Shen, N. V., Kreusch, A., Bellamy, H. D., & Pfaffinger, P. J. (1999) · Nature Structural Biology · doi:10.1038/4911 · Cited by 158 · see citing works
Structural Insights into the Protein Splicing Mechanism of PI-SceI
Poland, B. W., Xu, M., & Quiocho, F. A. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.22.16408 · Cited by 154 · see citing works
Loland, C. J., Nørregaard, L., Litman, T., & Gether, U. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032386299 · Cited by 151 · see citing works
Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase
Sankaranarayanan, R., Dock‐Brégeon, A., Rees, B., Bovée, M., Caillet, J., Romby, P., Francklyn, C. S., & Moras, D. (2000) · Nature Structural Biology · doi:10.1038/75856 · Cited by 149 · see citing works
The Carboxylate Shift in Zinc Enzymes: A Computational Study
Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2007) · Journal of the American Chemical Society · doi:10.1021/ja067103n · Cited by 147 · see citing works
Zn Protein Simulations Including Charge Transfer and Local Polarization Effects
Sakharov, D. V., & Lim, C. (2005) · Journal of the American Chemical Society · doi:10.1021/ja0429115 · Cited by 147 · see citing works
Campbell, E. A., Greenwell, R. S., Anthony, J. R., Wang, S., Lim, L., Das, K., Sofia, H. J., Donohue, T. J., & Darst, S. A. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.07.009 · Cited by 145 · see citing works
“Catalytic Zn2+ ions tend to be coordinated by His, Asp, and Glu (the ChrR-CLD Zn2+ has 3His and 1Glu ligands), whereas structural Zn2+ ions are prefer- entially coordinated by Cys (Alberts et al., 1998).”
BackgroundInfluentialMcLauchlan, C. C., Peters, B., Willsky, G. R., & Crans, D. C. (2015) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2014.12.012 · Cited by 141 · see citing works
Factors Governing Metal−Ligand Distances and Coordination Geometries of Metal Complexes
Kuppuraj, G., Dudev, M., & Lim, C. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp807972e · Cited by 142 · see citing works
Dudev, M., Wang, J., Dudev, T., & Lim, C. (2006) · The Journal of Physical Chemistry B · doi:10.1021/jp054975n · Cited by 141 · see citing works
Dudev, T., & Lim, C. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp0310347 · Cited by 140 · see citing works
Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins
Andreini, C., Bertini, I., & Cavallaro, G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026325 · Cited by 136 · see citing works
Parallel molecular mechanisms for enzyme temperature adaptation
Pinney, M. M., Mokhtari, D. A., Akiva, E., Yabukarski, F., Sanchez, D. M., Liang, R., Doukov, T. I., Martı́nez, T. J., Babbitt, P. C., & Herschlag, D. (2021) · Science · doi:10.1126/science.aay2784 · Cited by 136 · see citing works
“Consistent with this model, Cys ligands are more common at structural relative to catalytic Zn binding sites (46, 47).”
InfluentialCrystal Structure of a Superantigen Bound to the High-Affinity, Zinc-Dependent Site on MHC Class II
Li, Y., Li, H., Dimasi, N., McCormick, J. K., Martinꝉ, R., Schuck, P., Schlievert, P. M., & Mariuzza, R. A. (2001) · Immunity · doi:10.1016/s1074-7613(01)00092-9 · Cited by 135 · see citing works
Zinc-binding structure of a catalytic amyloid from solid-state NMR
Lee, M., Wang, T., Makhlynets, O. V., Wu, Y., Polizzi, N. F., Wu, H., Gosavi, P. M., Stöhr, J., Korendovych, I. V., DeGrado, W. F., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706179114 · Cited by 133 · see citing works
Treble clef finger--a functionally diverse zinc-binding structural motif
Grishin, N. V. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.8.1703 · Cited by 131 · see citing works
“Zinc is particularly important and is used for diverse functions, from catalytic to structural ( 1 ).”
BackgroundCarboxylate Binding Modes in Zinc Proteins: A Theoretical Study
Ryde, U. (1999) · Biophysical Journal · doi:10.1016/s0006-3495(99)77110-9 · Cited by 127 · see citing works
“Altogether, this explains why both bidentate and monodentate structures are common among zinc proteins (;30% of the Zn-carboxylate proteins are bidentate (Alberts et al., 1998), whereas among smaller zinc complexes,;10% are bidentate (Carrell et al., 1988)).”
BackgroundInfluentialPetersen, J. F. W., Cherney, M. M., Liebig, H., Skern, T., Kuechler, E., & James, M. N. G. (1999) · The EMBO Journal · doi:10.1093/emboj/18.20.5463 · Cited by 129 · see citing works
“(Alberts et al., 1998).”
BackgroundInfluentialPhysical Basis of Structural and Catalytic Zn-Binding Sites in Proteins
Lee, Y., & Lim, C. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.04.004 · Cited by 124 · see citing works
Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures
Patel, K., Kumar, A., & Durani, S. (2007) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2007.07.010 · Cited by 123 · see citing works
“The O–Zn–O angles are on the higher side for Eq–Zn–Ax when the bidentate arrangements are excluded, in accordance with the earlier reported observation [18].”
ResultHagelueken, G., Adams, T., Wiehlmann, L., Widow, U., Kolmar, H., Tümmler, B., Heinz, D. W., & Schubert, W. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510501103 · Cited by 122 · see citing works
Structure of the LpxC deacetylase with a bound substrate-analog inhibitor
Coggins, B. E., Li, X., McClerren, A. L., Hindsgaul, O., Raetz, C. R. H., & Zhou, P. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb948 · Cited by 122 · see citing works
Latent LytM at 1.3Å Resolution
Odintsov, S. G., Sabała, I., Marcyjaniak, M., & Bochtler, M. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.11.009 · Cited by 119 · see citing works
“This common, so-called elec-His-Zn motif orients the imidazole ring in space and is believed to make it more basic and thus a better ligand to the metal.(16) In H210, the imidazole N(1) coordinates the Zn2þ, and the N donates a hydrogen bond to the carbonyl oxygen of P200.”
BackgroundPrediction of transition metal‐binding sites from apo protein structures
Babor, M., Gerzon, S., Raveh, B., Sobolev, V. M., & Edelman, M. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21587 · Cited by 118 · see citing works
Molecular basis of Pirh2-mediated p53 ubiquitylation
Sheng, Y., Laister, R. C., Lemak, A. S., Wu, B., Tai, E., Duan, S., Lukin, J. A., Sunnerhagen, M., Srisailam, S., Karra, M., et al. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1521 · Cited by 116 · see citing works
“These nonexperimental distance restraints were developed based on analysis of the geometrical properties of zinc binding sites observed in a dataset of high-quality protein crystal structure”
MethodDNA apurinic-apyrimidinic site binding and excision by endonuclease IV
Garcin, E. D., Hosfield, D. J., Desai, S. A., Haas, B. J., Bjørås, M., Cunningham, R. P., & Tainer, J. A. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1414 · Cited by 114 · see citing works
“Notably, our E261Q Endo IV–AP DNA structure reveals that the Zn 3 coordination sphere is incomplet”
BackgroundDNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site
Li, C., Hor, L., Chang, Z.-F., Tsai, L., Yang, W., & Yuan, H. S. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg377 · Cited by 114 · see citing works
Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer
Der, B. S., Machius, M., Miley, M. J., Mills, J., Szyperski, T., & Kuhlman, B. A. (2011) · Journal of the American Chemical Society · doi:10.1021/ja208015j · Cited by 112 · see citing works
Hu, X., & Shelver, W. H. (2003) · Journal of Molecular Graphics and Modelling · doi:10.1016/s1093-3263(03)00153-0 · Cited by 112 · see citing works
Wanty, C., Anandan, A., Piek, S., Walshe, J. L., Ganguly, J., Carlson, R. W., Stubbs, K. A., Kahler, C. M., & Vrielink, A. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.06.029 · Cited by 110 · see citing works
Metal Selectivity Determinants in a Family of Transition Metal Transporters
Podar, D., Scherer, J., Noordally, Z. B., Herzyk, P., Nies, D. H., & Sanders, D. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.305649 · Cited by 110 · see citing works
“zinc proteases) (1, 2) or in substrate coordination (e.”
BackgroundAxelrod, H. L., Abresch, E. C., Paddock, M. L., Okamura, M. Y., & Fehér, G. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.4.1542 · Cited by 110 · see citing works
Zinc inhibition of monomeric and dimeric proton channels suggests cooperative gating
Musset, B., Smith, S. M. E., Rajan, S., Cherny, V. V., Sujai, S., Morgan, D., & DeCoursey, T. E. (2010) · The Journal of Physiology · doi:10.1113/jphysiol.2010.188318 · Cited by 109 · see citing works
“4 Å between Zn2+ and its coordinating atom (Alberts et al. 1998).”
BackgroundInfluentialAliès, B., Conte‐Daban, A., Sayen, S., Collin, F., Kieffer, I., Guillon, E., Faller, P., & Hureau, C. (2016) · Inorganic Chemistry · doi:10.1021/acs.inorgchem.6b01733 · Cited by 106 · see citing works
“42,60 We cannot (completely) exclude that a water molecule is the fourth ligand, because e ff ects on Asp1, Glu3, and Asp7 upon Zn(II) binding observed by NMR and XANES could be explained via H-bonding of these residues with the coordinating water.”
Corminbœuf, C., Hu, P., Tuckerman, M. E., & Zhang, Y. (2006) · Journal of the American Chemical Society · doi:10.1021/ja0600882 · Cited by 108 · see citing works
Defining Proximity Relationships in the Tertiary Structure of the Dopamine Transporter
Loland, C. J., Nørregaard, L., & Gether, U. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.52.36928 · Cited by 107 · see citing works
A General Strategy for the NMR Observation of Half-Integer Quadrupolar Nuclei in Dilute Environments
Lipton, A. S., Sears, J. A., & Ellis, P. D. (2001) · Journal of Magnetic Resonance · doi:10.1006/jmre.2001.2353 · Cited by 107 · see citing works
Burnett, J. C., Ruthel, G. T., Stegmann, C. M., Panchal, R. G., Nguyen, T. L., Hermone, A. R., Stafford, R. G., Lane, D. J., Kenny, T., McGrath, C. F., et al. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m608166200 · Cited by 106 · see citing works
Matsumoto, S., Shimada, A., Nyirenda, J., Igura, M., Kawano, Y., & Kohda, D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309777110 · Cited by 105 · see citing works
“Although zinc ions are usually four-coordinated in many metalloenzymes and zincfinger proteins (26), the six-coordination of the zinc ion is consistent with the fact that the six-coordinated Mg ion is reportedly a natural cofactor of OST (27).”
BackgroundSun, P., Ye, S., Ferrandon, S., Evans, T. C., Xu, M., & Rao, Z. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.09.039 · Cited by 103 · see citing works
“Zinc is coordinated in a T4 (tetrahedral) geometry by four residues, His48, Asp140, His110 (from a neighboring molecule) and the highly conserved residue Cys160 (Figure 4(a)).(34) The metal–donor atom target distances are all within accepted constraints.”
Lambert, S., Langley, D. R., Garnett, J. A., Angell, R. M., Hedgethorne, K., Meanwell, N. A., & Matthews, S. (2014) · Protein Science · doi:10.1002/pro.2456 · Cited by 100 · see citing works
“13 Å) for catalytic metal zinc-coordination sites.(35) The arrangement and proximity of residues Cys 142 and Cys 190 in our model and the presence of electron density in between the residues suggests the formation of a disulphide bridge, despite the presence of DTT in the crystallization buffer, with a distance betwee…”
BackgroundEngineered Proteins: Redox Properties and Their Applications
Prabhulkar, S., Tian, H. Q., Wang, X., Zhu, J., & Li, C.-Z. (2012) · Antioxidants and Redox Signaling · doi:10.1089/ars.2011.4001 · Cited by 96 · see citing works
“In catalytic sites, the zinc ion is usually exposed and bound to a solvent molecule (2).”
BackgroundGolovin, A., Dimitropoulos, D., Oldfield, T. J., Rachedi, A., & Henrick, K. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20288 · Cited by 98 · see citing works
“26”
Calculation and Prediction of Binding Free Energies for the Matrix Metalloproteinases
Donini, O., & Kollman, P. A. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm000040d · Cited by 95 · see citing works
Tholander, F., Muroya, A., Roques, B. P., Fournié‐Zaluski, M., Thunnissen, M. M. G. M., & Haeggström, J. Z. (2008) · Chemistry & Biology · doi:10.1016/j.chembiol.2008.07.018 · Cited by 94 · see citing works
Cross, J. B., Duca, J. S., Kaminski, J. J., & Madison, V. (2002) · Journal of the American Chemical Society · doi:10.1021/ja0201810 · Cited by 93 · see citing works
An Intersubunit Zinc Binding Site in Rat P2X2 Receptors
Nagaya, N., Tittle, R. K., Saar, N., Dellal, S. S., & Hume, R. I. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m504545200 · Cited by 93 · see citing works
Angiostatin and Endostatin: Endogenous Inhibitors of Tumor Growth
Sim, B. K. L., MacDonald, N. J., & Gubish, E. R. (2000) · Cancer and Metastasis Reviews · doi:10.1023/a:1026551202548 · Cited by 93 · see citing works
“One is that the tetrahedral coordination of the zinc ion by H1, H3, H11, and D76 strongly argues against a catalytic role for the zinc ion where one expects to have a water molecule [44]; secondly and more definitively, Endostatin protein that has the zinc binding ligands deleted and disrupted is still able to inhibit…”
BackgroundPlenge, P., Shi, L., Beuming, T., Te, J. A., Newman, A. H., Weinstein, H., Gether, U., & Loland, C. J. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.371765 · Cited by 92 · see citing works
“I179H 46 [41;52] 44 [40;48] 32 [29;36] 31 [30;33]”
Structure and dynamics of a primordial catalytic fold generated by in vitro evolution
Chao, F.-A., Morelli, A., Haugner, J., Churchfield, L. A., Hagmann, L. N., Shi, L., Masterson, L. R., Sarangi, R., Veglia, G., & Seelig, B. (2012) · Nature Chemical Biology · doi:10.1038/nchembio.1138 · Cited by 92 · see citing works
The Zinc proteome: a tale of stability and functionality
Sousa, S. F., Lopes, A., Fernandes, P. A., & Ramos, M. J. (2009) · Dalton Transactions · doi:10.1039/b904404c · Cited by 91 · see citing works
Robust recognition of zinc binding sites in proteins
Ebert, J. C., & Altman, R. B. (2007) · Protein Science · doi:10.1110/ps.073138508 · Cited by 90 · see citing works
“In addition, although many catalytic zincs are solvent exposed, the side chains of their coordinating residues may nonetheless be buried (Alberts et al. 1998).”
BackgroundHagelueken, G., Huang, H., Mainprize, I. L., Whitfield, C., & Naismith, J. H. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.026 · Cited by 90 · see citing works
A practical approach to docking of zinc metalloproteinase inhibitors
Hu, X., Baláž, Š., & Shelver, W. H. (2004) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2003.11.002 · Cited by 89 · see citing works
Fluorescence-based biosensing of zinc using carbonic anhydrase
Fierke, C. A., & Thompson, R. B. (2001) · BioMetals · doi:10.1023/a:1012980628412 · Cited by 87 · see citing works
“The preferred geometry of metal ions and the optimum ligand distances have been investigated in both model compounds and in proteins (Alberts & Nadassy 1998; Glusker 1991; Roe & Pang 1999; Rulisek & Vondrasek 1998).”
BackgroundInfluentialFletcher, P. L., Fletcher, M. D., Weninger, K., Anderson, T., & Martin, B. M. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.028365 · Cited by 86 · see citing works
Insights into the Mode of Action of a Putative Zinc Transporter CzrB in Thermus thermophilus
Cherezov, V., Höfer, N., Szebenyi, D. M. E., Kolaj‐Robin, O., Wall, J. G., Gillilan, R. E., Srinivasan, V., Jaroniec, C. P., & Caffrey, M. (2008) · Structure · doi:10.1016/j.str.2008.05.014 · Cited by 86 · see citing works
“The first concerns catalysis; the second structure stabilization (Alberts et al., 1998).”
BackgroundInfluentialElaC Encodes a Novel Binuclear Zinc Phosphodiesterase
Vogel, A., Schilling, O., Niecke, M., Bettmer, J., & Meyer‐Klaucke, W. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m112047200 · Cited by 86 · see citing works
Membrane Potential-controlled Inhibition of Cytochromec Oxidase by Zinc
Mills, D. A., Schmidt, B., Hiser, C., Westley, E., & Ferguson-Miller, S. M. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m111922200 · Cited by 86 · see citing works
Comparative analysis of editosome proteins in trypanosomatids
Worthey, E. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg870 · Cited by 85 · see citing works
“Zinc-centered domains have also been implicated in protein interaction (89).”
BackgroundZinc-mediated Allosteric Inhibition of Caspase-6
Velázquez-Delgado, E. M., & Hardy, J. A. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.397752 · Cited by 84 · see citing works
Tightening of the ATP‐binding sites induces the opening of P2X receptor channels
Jiang, R., Taly, A., Lemoine, D., Martz, A., Cunrath, O., & Grütter, T. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.75 · Cited by 83 · see citing works
“…these histidine residues, and the distance and angle measured between Zn 2 þ and the coordinating atom NE2 of the histidine residues were close to those obtained from the analysis of 111 crystal structures of Zn 2 þ -binding proteins available in the Protein Data Bank (PDB; Alberts et al , 1998).”
InfluentialIdentification and characterization of zinc-starvation-induced ZIP transporters from barley roots
Pedas, P., Schjoerring, J. K., & Husted, S. (2009) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2009.01.006 · Cited by 83 · see citing works
“For example, several motifs in transcriptional regulatory proteins are stabilized by Zn, including zinc finger domains, which require the binding of Zn for activation of transcription [4].”
BackgroundAnalysis of zinc‐ligand bond lengths in metalloproteins: Trends and patterns
Tamames, B., Sousa, S. F., Tamames, J. A. C., Fernandes, P. A., & Ramos, M. J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21536 · Cited by 82 · see citing works
Crystal Structure of Human Riboflavin Kinase Reveals a β Barrel Fold and a Novel Active Site Arch
Karthikeyan, S., Zhou, Q., Mseeh, F., Grishin, N. V., Osterman, A. L., & Zhang, H. (2003) · Structure · doi:10.1016/s0969-2126(03)00024-8 · Cited by 82 · see citing works
Chapman, R. P., & Bryce, D. L. (2007) · Physical Chemistry Chemical Physics · doi:10.1039/b712688c · Cited by 80 · see citing works
- Authors
- Alberts, I. L., Nadassy, K., & Wodak, S. J.
- Affiliations
- University of Stirling (GB)
- European Bioinformatics Institute (GB)
- Corresponding author
- Wodak, Shoshana J.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 1998-08
- Volume
- 7
- Issue
- 8
- Pages
- 1700-1716
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC2144076
- OpenAlex
- W2148386309
- Cited by
- 423
- References
- 93
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 8 · 2023: 10 · 2022: 10 · 2021: 11 · 2020: 11 · 2019: 11 · 2018: 11 · 2017: 13 · 2016: 18 · 2015: 16 · 2014: 19 · 2013: 11 · 2012: 23
- FWCI
- 14.55
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion)
- Funders
- European Bioinformatics Institute
- University of Stirling
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
- Keywords
- zinc binding site, zinc coordination geometry, primary coordination sphere, endopeptidase, hydrophobic residues, Protein Data Bank
- MeSH terms
- Aspartic Acid, Binding Sites, Catalysis, Chlorine, Cysteine, Glutamine, Histidine, Models, Molecular, Molecular Conformation, Nitrogen, Oxygen, Protein Binding, Sulfur, Zinc, Databases, Factual, Crystallography, X-Ray
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