Using different web servers on your refined structure is good thing to
do. But for distinguishing metal ion, specifically Mg, from water was
done unambiguously before these programs existed. The simple rule is two
fold: 1. distance; 2. coordination. For Mg ion distances are between 2
and 2.2 A and coordination is almost always nearly perfect octahedron.
Neither of those criteria met in your structure. Hence the verdict - it
is water.
Vaheh
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
jlliu liu
Sent: Monday, December 20, 2010 4:16 PM
To: [email protected]
Subject: [ccp4bb] Mg2+ or water
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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