Systematics in the interaction of metal ions with the main-chain carbonyl group in protein structures

Abstract

An analysis of the geometry of metal binding by peptide carbonyl groups in proteins is presented. Such metal ions are predominantly calcium in known protein structures. Cations tend to be located in the peptide plane, near the C = O bond direction. This distribution differs from that observed for water molecules bound to carbonyl oxygens. Most metal ions are bound to carbonyl oxygens of peptides in turns or in regions with no regular secondary structure. More infrequent binding interactions occur at the C-terminal end of α-helices or at the edges and sides of β-sheets, where the geometrical preferences of the metal-carbonyl interaction may be satisfied. In many proteins carbonyl groups that are one, two, or three residues apart along the polypeptide chain bind to the same cation; these structures show a limited number of main-chain conformations around the metal center.