Looks like Ni (II) in the 4-coordination tetrahedral config. Could it be loose Ni ions from the IMAC column if you’d used one? Ni and Mg have very close atomic radii and Ni (II) can form the 6-coordinate complex as well.
> On 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
> <mn_ion.png><mg_ion>
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