I would not rely only on coordination numbers, since Ca2+ can be also 
hepta-coordinated. You can look at the high resolution structures of 
parvalbumin and nucleoside hydrolases. And, although not up to date, this site 
is also useful http://mespeus.bch.ed.ac.uk/tanna/ . The anomalous map 
suggestion is probably the best way to go.


Dr. Massimo Degano
Biocrystallography Unit
Dept. of Immunology, Transplantation, and Infectious Diseases
DIBIT Fondazione San Raffaele
via Olgettina 58
20132 Milan - Italy
email: degano.mass...@hsr.it<mailto:degano.mass...@hsr.it>
phone: +39-0226437152
fax: +39-0226434153
skype: maxdegano
ORCID: 0000-0002-0787-1883

On 7 Mar 2018, at 20:27, Daniel M. Himmel, Ph. D. 
<danielmhim...@gmail.com<mailto:danielmhim...@gmail.com>> wrote:


Ca2+ usually is coordinated by five atoms, whereas Mg2+ usually is
coordinated by six.  I've seen that a lot in structures that I've determined.


On Wed, Mar 7, 2018 at 2:14 PM, Eleanor Dodson 
You just calculate a anom map - it doesnt need you to dselect Ca or Mg or 
anything else..
Judge the peak heights by the signal you get over any S sites in the model. The 
relative signal you expect depends on your wavelength of course.

On 7 March 2018 at 19:09, Rajesh Kumar 
<rajesh.p...@gmail.com<mailto:rajesh.p...@gmail.com>> wrote:
Hi Ivan,


suggest that Mg++ is the correct metal. Ca++ is not acceptable.

I am going to validate it by calculating anomalous peak for Ca++ too.

Thank you

On Wed, Mar 7, 2018 at 1:06 PM, Ivan Shabalin 
<iva...@iwonka.med.virginia.edu<mailto:iva...@iwonka.med.virginia.edu>> wrote:
Hi, Rajesh,

It does look like Ca to me. It has around 2.4 A distances to waters and quite 
many electrons (18), which correspond to rather wide and high density peak in 
the middle.

Mg has distances at 2.07, and 10 electrons (should be a smaller peak).

Na has 2.41 distances to waters, 10 electrons (should be a smaller peak).

After you place a metal and refine it, try using CheckMyMetal to validate it:


It takes into account preferable coordination geometries, coordination bond 
distances, and compares ADPs to average ADP for the surrounding atoms.

If the dataset is very good, and the wavelength of X-ray is rather long, you 
might even get anomalous signal for Ca:



With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park 
 Pinn Hall,Room 4223,
Charlottesville, VA 22908

On 03/06/2018 05:19 PM, Rajesh Kumar wrote:
Dear All,

Have you had experience with this kind of density? I am wandering what this 
could be?

Thank you very much for the help.



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