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
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http://www.uniklinik-freiburg.de/neuropathologie/live/forschung/ag-g-fritz.html
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