This database can display information on all the metal sites in one protein, specified by pdbcode, or on all the metal sites which contain a particular type of interaction such as Zn with histidine, or Ca with main chain carbonyl oxygen. The information displayed includes the distance, coordination number, resolution of the protein structure, and the full names, as given in the PDB file of the metal and the donor atom. The amino acid residues and other groups around any individual metal site can be displayed graphically. Distances, angles and coordination geometry are accessible.
The data has been extracted from PDB files for all protein structures determined with resolution 2.5 Å or better, and containing one or more of the metals Ag, Al, Au, Ba, Be, Ca, Cd, Co, Cr, Cs, Cu, Fe, Ga, Gd, Hg, Ir, K, Li, Mg, Mn, Mo, Na, Ni, Pb, Pd, Pr, Pt, Rb, Re, Rh, Ru, Sr, Tb, Tl, U, V, W, Y, Yb, and Zn. An atom (other than carbon or phophorus) is regarded as part of the metal site if it is within the target interaction distance (see Acta Cryst. D62 (2006) 678-682) plus a tolerance of 0.75 Å. The present version includes data up to May 2024; regular updating is intended. Metal and donor atom names, as in the PDB file, are stored in Tables, as well as distances, angles, occupancies and B values and some metal-metal distances; there are also details of the protein class, e.c. number, sequence, crystal data, resolution of the structure, R-factor, etc. The Tables may be interrogated directly with mysql, but the interface presented here allows a variety of convenient queries.
The search pages are fairly self explanatory. On the results page, clicking on the metal name will give graphical display and further information on the whole metal site. The controls next to the graphical display allow centring on the metal, display of donor atom names, display of angles or distances. Clicking on the pdbcode will give graphical display of the whole protein, crystal data and other information on the structure, including other metal sites. Many of the terms used are further defined or discussed in the series of papers listedtherein. Further information on Jmol, used for this graphical display may be found athttp://jmol.sourceforge.net/.
The results are obviously dependent on nomenclature and other quirks and details in the PDB files. Thus, for example, a search for Mg interactions with "O of water molecule" will not pick up the cases where the water molecule is described as being part of the het group MO6, rather than as HOH; they will appear instead in the category Mg interactions with "O of another non-protein molecule".
A PDB file usually only contains one asymmetric unit of a structure model. If a metal site is found on a rotation axis, the coordinating donor atoms might not be present as some donor atoms might be in the symmetry-related copies not presented in the PDB file. Symmetry-related asymmetric units can be generated by the symmetry operators and space group information defined in the PDB file. Among these generated symmetry-related copies, only one representative coordination group for each metal site is selected and stored in the database.
Metal "r.m.s.d." is the r.m.s. difference between metal-donor atom distances calculated from the PDB file coordinates, and the target distances (Acta Cryst. D62 (2006) 678-682). This is quite useful as a quality indicator for the reported distances and the geometry of the site. If r.m.s.d. is larger than, say 0.2 Å, it may be because the atom coordinates are poorly determined giving substantial bond length errors, and/or there are substantial real differences from expected geometry (as found for example in some bidentate carboxylates).
Metal donor atom interactions are only given when the donor atom occupancy is > 0.9, but the coordination numbers given may include donor atoms with lower occupancies; this accounts for some of the unexpectedly high coordination numbers listed. Information about coordination shapes is given as in Acta Cryst. D56 (2000) 857-867:
if coordination number is 6, the r.m.s. distortion from ideal octahedral is given, δ oct;
if coordination number is 5, the r.m.s. distortions given are δ tbp (from ideal trigonal bipyramidal) and δ tetp (from ideal tetragonal pyramidal);
if coordination number is 4, the r.m.s. distortions given are δ tet (from ideal tetrahedral) and δ sqp (from ideal square planar);
- obviously the smaller the value of δ the closer is the actual shape to the ideal description.