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:jlliu20022...@gmail.com>jlliu20022...@gmail.com> 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
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