[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: Ca2+ or Na+ ? at 2.3-2.8A bonding distances
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Dear Steven,
If the resolution of your dataset is high enough (better than 1.8 A is required)
and if you do not have any distance restraints (also anti bumping!) applied on
the distances in question, you could try to use the bond-valence method to
distinguish between Na+ and Ca2+.
There is only one formula:
Vi = sum {exp[(do-dij)/0.37]}
Vi is the so called valence sum of an atom i.
do is the standard single bond distance between your central atom and the ligand
in Angstroms (values are tabulated).
dij is the actually measured distance between your central atom i and the ligand
j in Angstroms.
0.37 is a scaling factor.
In your case, the do values are:
do(Ca-O)=1.967
do(Ca-N)=2.14
do(Na-O)=1.80
do(Na-N)=1.93
do values from Brese & O'Keeffe (1991) Acta Cryst. B47, 192-197.
So, all you have to do is to calculate the exp[(do-dij)/0.37] for each of the
five involved distances, using the correct do values, and sum them up. You
should do that twice, once with the do values for Ca and once with the do values
for Na.
If your central atom is Na, the valence sum for the Na case should be around 1,
while the summation for the Ca scenario would result in a value significantly
different from 2. If your metal is Ca the summation with the do-values for Ca
should give a valence of about 2, while the Na valence sum appears to be
different from 1.
You may also use the most recent version of SHELXPRO, where a very similar
method, the so called CBVS (Calcium Bond Valence Sum), is included. The program
performs all calculations automatically. The CBVS method is explained in detail
in a pulication which is going to be published in Acta D soon:
P. Müller, S. Köpke, G. M. Sheldrick (2002) Acta Cryst. D58, in press.
I many cases, the bond-valence method can give rise to very helpful information.
However, the resolution as absolutely critical. In addition you have to be sure
about the completenes of the co-ordination sphere and the occupancy of the
ligands, as well as their nature. The occupancy of the metal atom should be 1
too.
I hope this helps
best wishes
Peter
"Q. Steven Xu" <qian@med-biophg.bu.edu> said:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> I think the similar topic has been discussed on this bulletin board. But I
> just want to get more comments on how to distinguish between Ca2+ and Na+?
>
> I found a cation binding site in a pentagonal pyramidal arrangement.
> A quite weak resdiual positve peak can be seen on the opposite side, which
> could be another water molecule forming a pentagonal bipyramidal
> coordination. The distances are in a range of 2.3~2.8A with the average
> around 2.45A, thereby K+ was excluded due to its coordination distance of
> around 2.8A. The only possibility then fall down on Na+ or Ca2+ present in
> the crystallization buffer. The concentration of Na+ was much higher than
> Ca2+. Thus I think it is more likely to be a Na+. But is there any other
> arguments to prove this? I don't think they can be distinguished by bond
> distances, because in both cases they are around 2.4A. Or by anomalous
> difference map? The data was collected at 13466ev (0.92973A). I don't see
> much anomalous difference on both elements at this wavelength.
>
> Thanks in advance.
>
> regards,
> Q. Steven Xu
> Dept. of Physiology and Biophysics
> Boston Univ. School of Medicine
> Tel: (617)638-4083
> Fax: (617)638-4041
> E-mail: qian@med-biophg.bu.edu
>
--
************************************************************************
Dr. Peter Mueller fon: +1-310-825-1402
UCLA-DOE Laboratory of Structural Biology fax: +1-310-206-3914
and Molecular Medicine
205 MBI
BOX 951570 http://shelx.uni-ac.gwdg.de/~peterm
Los Angeles CA 90095-1570 peterm@mbi.ucla.edu
************************************************************************