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 Å 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'
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