Check the anomalous difference map on these sites.
Thanks
Abhinav
Abhinav Kumar
JCSG @ SSRL, MS 99
2575 Sand Hill Road
Menlo Park, CA 945025-7015
Phone: 650 926 2992
Fax: 650 926 3292
On May 27, 2008, at 6:38 PM, Bernhard Rupp wrote:
Dear All,
something one/some of you might have seen already and
might know what it might be/how to analyse:
Material: dimer of Se-Met, Ni-purified, NaCl and NaAc in
purification history.
I have 4 'waters', 2 each in the same monomer location
in a dimer of 2.5A Se-Met structure. They are multiple
coordinated - perhaps dist octahedron - and refine down to
B=2.0 and show correspondingly strong density. Surrounding
protein Bs range from 15 backbone to 37 Arg sidechain
First idea of course metal ions.
But the distances are odd - 3.1 to 3.7, unusually long for
common metal coordination.
If I use Na+/Mg++, the Bs still refine down to 4 to 6
K+ B's run up to ~25, Ni++ to 35-40, could be partial occ.
Given the charge distribution I doubt Cl- makes sense -
it sure looks like a nice place for cation. Not enough space
for sul- and fos-fates.
No experiments possible, have to deal with what's on hand.
Images on web:
http://www.ruppweb.org/images/snap.gif
http://www.ruppweb.org/images/mystery_ion.gif
How common are such large coordination distances in protein/metal
coordination and are there any (in silico) analysis tools one could
use?
Thx, br
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Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
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http://www.ruppweb.org/
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