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
Dept. of Immunology, Transplantation, and Infectious Diseases
DIBIT Fondazione San Raffaele
via Olgettina 58
20132 Milan - Italy
On 7 Mar 2018, at 20:27, Daniel M. Himmel, Ph. D.
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
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
suggest that Mg++ is the correct metal. Ca++ is not acceptable.
I am going to validate it by calculating anomalous peak for Ca++ too.
On Wed, Mar 7, 2018 at 1:06 PM, Ivan Shabalin
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
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.
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:
Have you had experience with this kind of density? I am wandering what this
Thank you very much for the help.
Rispetta l'ambiente: non stampare questa mail se non ? necessario.
Respect the environment: if it's not necessary, don't print this mail.