>Sorry, the attachment is in here.
Doesn't look like Mg2+ at all. Distances are too long, Mg is never
coordinated by amides and if it were Mg you would have seen waters around it.
Looks like tightly bound water to me.
- Dima
>On Mon, Dec 20, 2010 at 4:16 PM, jlliu liu
><<mailto:[log in to unmask]>[log in to unmask]> 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
>
>
>
>Content-type: image/png; name=367-mgtest.png
>Content-disposition: attachment; filename=367-mgtest.png
>X-Attachment-Id: f_ghy0k5e31
>
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