Classification of mononuclear zinc metal sites in protein structures

摘要

Our study of the extended metal environ- ment, particularly of the second shell, focuses in this paper on zinc sites. Key findings include: (i) The second shell of mononuclear zinc centers is generally more polar than hydro- phobic and prominently features charged residues engaged in an abundance of hydrogen bonding with histidine ligands. Histidine-acidic or histidine-tyrosine clusters commonly overlap the environment of zinc ions. (ii) Histidine tautomeric metal bonding patterns in ligating zinc ions are mixed. For example, carboxypeptidase A, thermolysin, and sonic hedge- hog possess the same ligand group (two histidines, one unibidentate acidic ligand, and a bound water), but their histidine tautomeric geometries markedly differ such that the carboxypeptidase A makes only N~δ1 contacts, thermolysin makes only N~ε2 contacts, and sonic hedgehog uses one of each.