Dear Jacob, Another publication I found useful on this topic:
Is the bond-valence method able to identify metal atoms in protein structures? Mueller et al. (2003). Acta Crystallogr. D59, 32-7. https://www.ncbi.nlm.nih.gov/pubmed/12499536 Best regards, Navdeep --- On Thu, Mar 06, 2014 at 07:45:25PM +0000, Keller, Jacob wrote: > Dear Crystallographers, > > 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... > > All the best, > > Jacob Keller > > > ******************************************* > Jacob Pearson Keller, PhD > Looger Lab/HHMI Janelia Farms Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > email: kell...@janelia.hhmi.org > ******************************************* --- Navdeep S. Sidhu Departments of Structural Chemistry & Neuropediatrics University of Goettingen, Germany ---
