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Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):678-82. Epub 2006 May 12.

Small revisions to predicted distances around metal sites in proteins.

Author information

1
Institute of Structural and Molecular Biology, Michael Swann Building, University of Edinburgh, Edinburgh EH9 3JR, Scotland. marjorie.harding@ed.ac.uk

Abstract

A new analysis has been made of distances around metal sites in protein structures in the Protein Data Bank determined with resolution < or =1.25 A and equivalent distances have been extracted from the Cambridge Structural Database. They are for the metals Na, Mg, K, Ca, Mn, Fe, Co, Cu, Zn and the donor atoms O of water, O of Asp and Glu, O of the main-chain carbonyl group, N of His and S of Cys. Some revisions are recommended to the tables of 'target distances' previously given. As well as small changes in many distances and a large improvement for Mg-O(carboxylate), the table includes an indication of how reliable each prediction may be. Special attention was given to carboxylate interactions. When the carboxylate group is monodentate, the M-O(carboxylate) distance is well defined, but for bidentate carboxylate groups a wide range of distances is allowable; when the metal is Co, Cu or Zn the M-O(1) and M-O(2) distances are clearly inversely correlated; for the more purely electrostatic interactions involving Na, K and Ca there is a wider scatter of distances and little correlation.

PMID:
16699196
DOI:
10.1107/S0907444906014594
[Indexed for MEDLINE]

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