Hi Rajesh, You may find this database is also useful while refining your model
http://mespeus.bch.ed.ac.uk/MESPEUS_10/ and for calcium http://mespeus.bch.ed.ac.uk/MESPEUS_10/_5.jsp Abhik On Tue, Mar 6, 2018 at 10:59 PM, Patrick Loll <pjl...@gmail.com> wrote: > Calcium likes to form octahedral complexes with water (or other > oxygen-containing) ligands. This looks like a classic example. > > After you model and refine this, you’ll want to check water-metal > distances, to make sure they are appropriate for calcium. There is a nice > literature on such things, which I of course don’t have at my fingertips; > but I think Wladek Minor has done some data-mining in metal-containing > protein structures, and Amy Katz and Jenny Glusker have a number of papers > that are relevant. There are more, of course—a little time in the “library” > is warranted. > > Cheers, > > Pat Loll > > > On 6 Mar 2018, at 5:19 PM, Rajesh Kumar <rajesh.p...@gmail.com> wrote: > > > > Dear All, > > > > Have you had experience with this kind of density? I am wandering what > this could be? > > > > Thank you very much for the help. > > > > -Rajesh > > > > > > <Screen Shot 2018-03-06 at 5.15.20 PM.png> > > > > ------------------------------------------------------------ > --------------------------- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pjl...@gmail.com > pj...@drexel.edu >
