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Re: [ccp4bb]: Ca2+ or Na+ ? at 2.3-2.8A bonding distances



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"Q. Steven Xu" wrote:
> 
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> 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,


 There is a big difference in the anom signal..


 NA          0.9300     0.0508     0.0440     
 S           0.9300     0.1682     0.2115
 CA          0.9300     0.2780     0.5127


You can use your S which are usually visible in DANO maps at this
wavelength to monitor the signal. CA should stand out like a sore thumb.

NA of the same order as O or C will be invisible..

 Eleanor

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

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