METAL COORDINATION SITES IN PROTEINS

(last updated August 2011)

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 determined by diffraction methods.  It deals with the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu, Zn,  but in some applications excludes three commonly recurring types of group - haem groups, Fe/S clusters, and chlorophyll (Mg) groups.

 

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

The database is now updated at MESPEUS_10

MESPEUS_10 includes contact distances and geometry around metal sites in proteins, derived from protein structures in the PDB up to January 2010, determined to a resolution of 2.5 or better.

The database is described by K.Hsin, Y.Sheng, M.M.Harding, P.Taylor, M.D.Walkinshaw in J Applied Crystallography 41 (2008) 963-968 .

 

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

 

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

 

4. 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).

 

 

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

 

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'        

and a review

Crystallography Reviews 16 (2010) 247-302. M.M.Harding, M.W.Nowicki, M.D.Walkinshaw 'Metals in Protein Structures: a review of their principal features'

 

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

Centre for Translational and Chemical Biology,

University of Edinburgh,

Michael Swann Building, Mayfield Road,

Edinburgh EH9 3JR, Scotland

email     Marjorie.Harding @ ed.ac.uk