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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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Eleanor J.Dodson, York Structural Biology Laboratory,
Chemistry Department,
University of York, Y01 5DD Heslington, U.K.
Tel: Work: +44 (1904) 32 82 53 Home +44 (1904) 42 44 49
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