The DOI matches its Crossref record; 94 of the 94 references it cites were found in a registry or an index.
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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“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 AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins (2014) · cites this paper as [16]
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Synthetic Analogues Relevant to the Structure and Function of Zinc Enzymes
Parkin, G. (2004) · Chemical Reviews · doi:10.1021/cr0206263 · Cited by 944
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AlphaFill: enriching AlphaFold models with ligands and cofactors
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Background
Metadata
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › 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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