METAL COORDINATION SITES IN PROTEINS

(last updated May 2008)

This website assembles information about the geometry and constitution of metal coordination groups in metalloproteins;  the information is derived from protein crystal structures in the Protein Data Bank (PDB) which have been detrermined by diffraction methods.  It deals with the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu, Zn,  but in most applications excludes three commonly recurring types of group - haem groups, Fe/S clusters, and chlorophyll (Mg) groups.

NEW : MESPEUS : A Database of the Geometry of Metal Sites in Proteins

This includes contact distances and geometry around metal sites in proteins, derived from protein structures in the PDB determined to a resolution of 2.5 Å or better - new 2008.

1. Quick Guide to characteristics of metal sites in proteins - new February 2005.

2. Target distances for different metal-donor atom combinations, for use in validation or refinement of metalloprotein structures - revised July 2006.

3. Listing of individual metal sites - amino-acid donors, their relative positions in the protein sequence, other non-protein donors, conformation of chelate loops, etc - in a representative set of metalloproteins, based on the PDB up to September 2003.

NEW lists for 10 metals based on PDB up to Jan 2007        (added Nov 2007, some corrections Sep 2008).

4. For each metal, Tables summarising the frequency of occurrence of different coordination numbers, donor groups, etc , in the listings above (new 2005).

5. MESPEUS : A Database of the Geometry of Metal Sites in Proteins

This includes contact distances and geometry around metal sites in proteins, derived from protein structures in the PDB determined to a resolution of 2.5 Å or better. A paper is being submitted to J. Appl. Cryst. (K.Hsin, Y.Sheng, M.M.Harding, P.Taylor, M.D.Walkinshaw) - May 2008.

6. Papers which have lead to the tables and comments above.

Acta Cryst. D55 (1999) 1432-1443.          'The geometry of metal-ligand interactions relevant to proteins' I

Acta Cryst. D56 (2000)   857-867.           'The geometry of metal-ligand interactions relevant to proteins. II. Angles at the                                                                                                                   metal atom, additional weak metal-donor interactions'

Acta Cryst. D57 (2001) 401-411.             'Geometry of metal-ligand interactions in proteins'                        

Acta Cryst. D58 (2002) 872-874.             'Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium' 

Acta Cryst. D60 (2004) 849-859.             'The architecture of metal coordination groups in proteins'             

Acta Cryst. D62 (2006) 678-682.             'Small revisions to predicted distances around metal sites in proteins'        

7. Some other websites of relevance to metalloproteins.

8. A note about metal-phosphate interactions in metalloproteins ( March 2005).

9. Older material: individual metal coordination groups - details of donors, metal-donor distances, occupancies, B-values, coordination numbers and distortions, for all metal coordination groups in a representative set of protein structures in the PDB in July 2001.

10. Deposited tables for the paper above,  'Architecture of metal coordination ...'

Marjorie M Harding

Structural Biochemistry Group

School of Biological Sciences

University of Edinburgh

Mayfield Road, Edinburgh EH9 3JR, Scotland.

email:  Marjorie.Harding @ ed.ac.uk