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ZincBind-the database of zinc binding sites
Sam M Ireland1, Andrew C R Martin1
1Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, UK.
Database : the Journal of Biological Databases and Curation
|February 6, 2019
Summary
ZincBind is a new database that identifies and catalogs zinc binding sites in proteins. This resource aids researchers by providing comprehensive data on zinc
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Zinc is a critical metal ion involved in numerous biological processes, including catalysis, structural stability, gene expression, and immunity.
- A significant portion of the human genome encodes zinc-binding proteins, highlighting zinc's biological importance.
- Currently, no centralized resource exists to systematically identify and present all known zinc-binding sites in proteins.
Purpose of the Study:
- To develop and present ZincBind, a comprehensive database of zinc-binding sites in proteins.
- To provide a user-friendly web interface for accessing, browsing, and downloading zinc-binding site data.
- To establish a regularly updated resource for the scientific community.
Main Methods:
- Utilized structural data from the Protein Data Bank (PDB) to identify all instances of zinc-protein interactions.
- Developed algorithms to pinpoint specific zinc-binding sites within protein structures.
- Implemented a clustering approach based on 90% sequence identity to group similar binding sites.
Main Results:
- The ZincBind database currently contains 24,992 identified zinc-binding sites.
- These sites have been clustered into 7,489 unique representative sites.
- The database is accessible via a web interface and a REST API for data retrieval and integration.
Conclusions:
- ZincBind offers a valuable, centralized resource for researchers studying zinc-protein interactions.
- The database facilitates the exploration of zinc's roles in biological functions by providing structured data on binding sites.
- Ongoing updates will ensure ZincBind remains a current and comprehensive repository for zinc-binding site information.
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