Hi, once upon a time I found myself interested in this topic, which prompted my to read these papers:
1993 Gregory 2004 Harding 1996 Nayal 2005 Babor 1998 Rulisek 2005 Sommerhalter 1999 Harding 2006 Dudev 2000 Harding 2006 Harding 2000 Harding_2 2006 Stefan 2001 Pidcock 2007 Tamames 2002 Harding 2007 Weiss 2002 Mueller 2008 Goyal 2002 Thaimattam 2008 Hsin 2002 Weiss 2008 Seebeck 2003 Dudev 2008 Zheng_Minor 2009 Hemavathi I should say that was rewarding! (P.S.: Sorry, I did not bother to open each PDF and copy the full article citation, instead just fetched year and name with a script. Those who interested can find these papers on the web or I can send more details off list) All the best, Pavel On Sat, Mar 8, 2014 at 12:54 PM, Navdeep Sidhu <nsi...@shelx.uni-ac.gwdg.de>wrote: > 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 > --- >
