Send to

Choose Destination
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

Institute of Structural and Molecular Biology, Michael Swann Building, University of Edinburgh, Edinburgh EH9 3JR, Scotland.


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.

[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for International Union of Crystallography
Loading ...
Support Center