The geometry of metal-ligand interactions relevant to proteins. II. Angles at the metal atom, additional weak metal-donor interactions.
Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from 'small-molecule' structures determined by X-ray or neutron diffraction to an accuracy and precision much better than that of most current protein structure determinations. Structures of Mg, Mn, Fe, Cu and Zn complexes with ligands whose donor atoms may be only N, O, S or Cl have been selected and analysed in terms of the geometry of the metal coordination group - octahedral, tetrahedral, tetragonal pyramidal etc. The r.m.s. deviation of all the interbond angles around the metal atom provides a measure, delta, of the deviation from ideal geometry. Average values of delta are tabulated for the different metals in each type of complex. For simple non-chelated complexes of Mn, Fe and Zn, distortions of up to 5 degrees in octahedral complexes and 10 degrees in tetrahedral complexes are found to be normal and seem likely to be a consequence of packing effects, ligand bulk or intramolecular effects. Substantially larger distortions are found for some other metals and geometries and are common for chelated complexes. Brief comments on six-, seven- and eight-coordinate Ca complexes are included. Tables are also presented showing that for four- and five-coordinate complexes of Zn and Cu it is quite common to find additional weakly coordinated ligands, usually with N or O donor atoms and with M.N,O distances longer than a normal bond length but shorter than a van der Waals contact, e.g. in the range 2.4-3.0 A for Zn and 2.6-3.0 A for Cu. Although the contributions to bond valency or bonding energy of such interactions may not be great, their effect on geometry can be considerable; they can, for example, cause much larger distortions of tetrahedral Zn complexes than indicated above.
Institute of Cell and Molecular Biology, University of Edinburgh, Michael Swann Building, Edinburgh EH9 3JR, Scotland. marjorie. harding@ed.ac.uk.
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Harding
D002614:Chelating Agents / Q000737:chemistry; D008024:Ligands; D008667:Metalloproteins / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*
D002614:Chelating Agents; D008024:Ligands; D008667:Metalloproteins; D008670:Metals