On Thu, Mar 6, 2014 at 11:45 AM, Keller, Jacob <[email protected]>wrote:
> I was curious whether there has been a rigorous evaluation of ion binding > sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine > that there is a considerably broad spectrum of habits and rigor in > assigning solute blobs to ion X or water, and in fact it would be difficult > in many cases to determine which ion a given blob really is, but there > should be at least some fraction of ions/waters which can be shown from the > x-ray data and known geometry to be X and not Y. This could be by small > anomalous signals (Cl and H2O for example), geometric considerations, or > something else. Maybe this does not even matter in most cases, but it might > be important in others... > A couple of references: http://www.ncbi.nlm.nih.gov/pubmed/18614239 http://www.ncbi.nlm.nih.gov/pubmed/24356774 Anecdotally, it is not difficult to find incorrect structures; in fact, one of mine has "magnesium" ions at crystal contacts with big Fo-Fc and anomalous map peaks, and I know it's not the only such structure in the PDB. However, while there are plenty of examples that are clearly wrong, it is difficult to come up with strict rules that apply to typical MX data - at 3Å resolution (or even better), a native Zn-binding site might have bond valences that are just awful. This doesn't mean the metal assignment is wrong. The placement of waters alone has a huge impact on such calculations. -Nat
