Cited by 426Enzyme Structure and FunctionProtein Structure and DynamicsCrystal structures of chemical compounds

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Analysis of zinc binding sites in protein crystal structures

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Alberts, Ian L., Nadassy, Katalin, Wodak, Shoshana J.·1998·Protein Science

DOI 10.1002/pro.5560070805PMC PMC2144076

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Abstract

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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Authors: Alberts, I. L., Nadassy, K., & Wodak, S. J.
Affiliations: University of Stirling (GB)
European Bioinformatics Institute (GB)
Corresponding author: Wodak, Shoshana J.
ORCID: Alberts, Ian L.
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
DOI: 10.1002/pro.5560070805
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
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor, 3805 d)
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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Analysis of zinc binding sites in protein crystal structures

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