About the Database

ZincBind is a database of zinc binding site structures, automatically generated from the Protein Data Bank.

For every PDB structure which contains at least one zinc atom, ZincBind identifies the liganding residues and creates a binding site for the zinc - with liganding residues defined as those with a relevant atom within 3 Angstroms of the zinc.

If two zinc atoms share a liganding residue, or if a zinc atom shares a liganding residue with some other metal ion, these are clustered together into a single multi-metal site.

The chains associated with each zinc site are stored, and clustered on 90% sequence identity. These clusters are then used to cluster the Zinc Sites themselves - where two sites belong to the same cluster if they are associated with the same chain cluster(s) and have the same binding residue identifiers.