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The Extended Environment of Mononuclear Metal Centers in Protein Structures
Samuel Karlin, Zhan-Yang Zhu and Kenneth D. Karlin
Proceedings of the National Academy of Sciences of the United States of America
Vol. 94, No. 26 (Dec. 23, 1997), pp. 14225-14230
Published by: National Academy of Sciences
Stable URL: http://www.jstor.org/stable/43599
Page Count: 6
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The objectives of this and the following paper are to identify commonalities and disparities of the extended environment of mononuclear metal sites centering on Cu, Fe, Mn, and Zn. The extended environment of a metal site within a protein embodies at least three layers: the metal core, the ligand group, and the second shell, which is defined here to consist of all residues distant less than 3.5 angstrom from some ligand of the metal core. The ligands and second-shell residues can be characterized in terms of polarity, hydrophobicity, secondary structures, solvent accessibility, hydrogen-bonding interactions, and membership in statistically significant residue clusters of different kinds. Findings include the following: (i) Both histidine ligands of type I copper ions exclusively attach the Nδ 1 nitrogen of the histidine imidazole ring to the metal, whereas histidine ligands for all mononuclear iron ions and nearly all type II copper ions are ligated via the Nε 2 nitrogen. By contrast, multinuclear copper centers are coordinated predominantly by histidine Nε 2, whereas diiron histidine contacts are predominantly Nδ 1. Explanations in terms of steric differences between Nδ 1 and Nε 2 are considered. (ii) Except for blue copper (type I), the second-shell composition favors polar residues. (iii) For blue copper, the second shell generally contains multiple methionine residues, which are elements of a statistically significant histidine-cysteine-methionine cluster. Almost half of the second shell of blue copper consists of solvent-accessible residues, putatively facilitating electron transfer. (iv) Mononuclear copper atoms are never found with acidic carboxylate ligands, whereas single Mn2+ ion ligands are predominantly acidic and the second shell tends to be mostly buried. (v) The extended environment of mononuclear Fe sites often is associated with histidine-tyrosine or histidine-acidic clusters.
Proceedings of the National Academy of Sciences of the United States of America © 1997 National Academy of Sciences