Hi Dilip, More information is needed regarding the crystallization condition(s). Anyway, Mg2+ ions are always (most of the time) are surrounded by water molecules in their primary hydration sphere...(typical distance should be 2.2 A, if I remember correctly)...and the typical geometry would be octahedral (could be distorted sometime)...or very rarely tetrahedral (we found once..)..Try fitting Mg2+ along with waters...keeping the proper metal water distances and the coordination geometry...and then refine..Good luck...!!!
HTH Sudipta. On Thu, Jul 9, 2015 at 9:41 AM, Gyanendra Kumar <[email protected]> wrote: > Dear Dilip, > > I was wondering if the problem was more basic, just about setting the > occupancy in your input pdb file. Try setting the occupancy of Mg to 1 in > your input coordinate file (pdb file) and refine it. If its Mg, it should > turn blue. If its not Mg, the density should turn red instead of staying > green, or may be partially green. > Next, try Mn with occupancy 1 in the input file. Did you have Calcium > chloride in your crystallization condition? You could try Ca as well. > > -Gyan > > On Thu, Jul 9, 2015 at 4:35 AM, Dilip Kumar <[email protected]> wrote: > >> Dear All >> >> I have solved a structure of a metal-ion dependent exonuclease enzyme. In >> homologous structures, two or three Manganese ions are present at catalytic >> center. However, I have used 2 mM MgCl2 in protein purification buffer. I >> tried to fit both of these metal ions at catalytic center but in both cases >> it still shows green density (Sigma level ~ 7) in difference map and low >> b-factor (<10) for these metal ions. For better understanding I have >> attached the screenshot of metal ions with difference map on. Please >> suggest me the possible reasons or methods to validate the presence of any >> other metal ions at catalytic center. >> >> Thanks in advance. >> >> Regards >> Dilip Kumar >> Research Associate >> Chemical and Systems Biology Unit >> CSIR-Institute of Genomics & Integrative Biology >> Delhi-110025 >> > > > > -- > Gyanendra Kumar, PhD > St. Jude Children's Research Hospital, > Department of Structural Biology, > 262, Danny Thomas Place, MS-311 > Memphis, TN 38105 > Phone: 901-595-3839 > Cell: 631-875-9189 > ------------------------------------------------------- >
