Dear Kristof,
The following literature can be a start point for you.
/Acta Cryst./ (2003). D*59*, 32-37
Is the bond-valence method able to identify metal atoms in protein
structures?
P. Müller
<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=M%26uuml;ller,%20P.>,
S. Köpke
<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=K%26ouml;pke,%20S.>
and G. M. Sheldrick
<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Sheldrick,%20G.M.>
*Abstract:* The proper assignment of metal ions in X-ray structures of
proteins is not always easy, but in many cases this knowledge can be
important, /e.g./ for an understanding of enzyme mechanism. In this
publication, the bond-valence approach is assessed critically. A
simplified version, the calcium bond-valence sum (CBVS), is proposed for
the convenient analysis of the geometric environment of potential sites
with a view to metal-ion assignment. The bond-valence approach is found
to be more reliable for structures determined from high-resolution data
(1.5 Å or better).
*Keywords: bond-valence method
<http://scripts.iucr.org/cgi-bin/full_search?words=bond-valence%20method&Action=Search>;
CBVS
<http://scripts.iucr.org/cgi-bin/full_search?words=CBVS&Action=Search>;
metal ions in proteins
<http://scripts.iucr.org/cgi-bin/full_search?words=metal%20ions%20in%20proteins&Action=Search>;
validation
<http://scripts.iucr.org/cgi-bin/full_search?words=validation&Action=Search>;
/SHELXPRO/
<http://scripts.iucr.org/cgi-bin/full_search?words=SHELXPRO&Action=Search>.*
Kristof Van Hecke wrote:
Dear all,
I'm looking for some means (literature references,.. possible
programs) to differentiate between cations (Na+), anions (e.g. Cl-)
and water molecules in high resolution protein/DNA structures, based
on B-factors, distances, coordination, etc..
Does anyone has got an idea of what's the best strategy to follow in
these cases..?
many thanks
Kristof
--------------------------------------
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
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