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 <[log in to unmask]> 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
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