If it's more than likely Mg and it's easy to grow crystals, try
soaking/cogrowing BaCl2/BaOAc. At least in the RNA world, Mg sites can
easily be displaced by Ba. The latter of course has anomalous signal
on the home sources. Place your divalents using the anomalous diff map.
Have no clue what this .odp file ext is so I can't view the png.
F
On Dec 20, 2010, at 2:16 PM, 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>
---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
