Hi,
you might have a look into the papers of MM Harding. There is a series
of papers about metal ions in X-ray structures in Acta D.
Look at the number of coordination, geometry and distances. Then you can
easily decide whether there is a metal ion and which metal ion it might be.
And of course the peak height of anomalous signal (e.g Ca2+, K+) is a
hint, but one has to be careful in the case there is not full occupancy.
HTH
Guenter
*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
--
***********************************
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
e-mail: [email protected]
e-mail: [email protected]
http://www.uniklinik-freiburg.de/neuropathologie/live/forschung/ag-g-fritz.html
Tel.: +49 761 270 5078
Fax.: +49 761 270 5050
