and for calciumHi Rajesh,You may find this database is also useful while refining your model
http://mespeus.bch.ed.ac.uk/MESPEUS_10/ AbhikOn Tue, Mar 6, 2018 at 10:59 PM, Patrick Loll <[log in to unmask]> 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 <[log in to unmask]> 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>
>
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