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A PDB/CSD study of the metalloenzyme HisHisX-M-X type active sites and their low weight model complexes

The Cambridge Structural Database (CSD) [ ] was searched for metal complexes of six transition biometals (Zn, Cu, Cd, Co, Fe and Ni), with overall coordination number 4, and where three coordination valences are captured by a tridentate (chelating) ligand while the remaining one binds a monodentate ligand. In the extracted set of complex structures, the electron donor atoms array in the tridentate ligand was restricted to NNX (where X = N, O or S). This arrangement is a structural model of a typical mononuclear metalloenzyme active site, where metal is embedded in a trihystidine, dihystidine-monocarboxylate or dihystidine-monocysteinate coordination core, and where its remaining free coordination valence is set aside for a reversible substrate binding. The set of mononuclear metalloenzymes with the catallytic site of the type L-M-HHX, where L = substrate, M = metal ion, H = hys, and X = hys, asp, glu or cys) was extracted from PDB [ ], and the catalytic sites geometries were analyzed. The representation of particular metal ions in this type of coordination environment was analyzed in both enzymes and complexes of low molecular weight. In both sets (from CSD and from PDB), the prevalence of the tetrahedral or square-planar coordination sphere was analyzed, with respect to i) the central metal ion, and ii) the specific electron donor atom. The bond lengths of the coordination contacts were analyzed and compared with respect to the chemical and electronic environment of the donor atom. The organic ligands used to mimic this type of metalloenzyme active site were reviewed, and the particular coordination geometry enforced by each one of the ligand types was analyzed.

CSD; PDB; metalloenzyme; low weight models

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