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.
Max -- 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: Rajesh, 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. -Daniel On Wed, Mar 7, 2018 at 2:14 PM, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote: 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. Eleanor On 7 March 2018 at 19:09, Rajesh Kumar <rajesh.p...@gmail.com<mailto:rajesh.p...@gmail.com>> wrote: Hi Ivan, https://csgid.org/csgid/metal_sites/ 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 Rajesh 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: https://csgid.org/csgid/metal_sites/ 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: http://skuld.bmsc.washington.edu/scatter/AS_periodic.html Ivan With best regards, Ivan Shabalin, Ph.D. Research Scientist, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue<https://maps.google.com/?q=1340+Jefferson+Park+Avenue&entry=gmail&source=g>, 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. -Rajesh ---- Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail.
