Mg2+ is (almost) aways octahedrally coordinated, usually by oxygen atoms, with distances of ~2A.
Phil
On 20 Dec 2010, at 21:16, jlliu liu wrote:
> Hi All,
>
> I am refining a structure and encountered a problem of modeling a difference density as water or Mg2+, and would like to hear opinions from the community. It has the following coordinations (attached): the water/Mg2+ forms salt bridge/H-bonding interaction with a carboxylate group from the ligand, it also forms salt bridge/H-bonding interaction with a Glu residue from the protein, it is also within hydrogen bonding distance to the main chain N of another protein residue. In provious publication, it was modelled as a Mg2+ and the author reasoned the dual salt-bridge stabilizes the liganding binding, also the Mg2+ is present in the protein solution for crystallization. For my case, I have no Mg2+ present in the protein buffer, also modelling it with water refines perfectly with no indication of positive difference density even at 2.0 sigma cut off. Should I modelled this density as water or as Mg2+. Your opinions are appreciated.
>
> JL
>
>
> <test.png.odp>
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