Anomalous map might give you some idea if it can be zinc.
Pharmaceutical Sciences, Department of Biosciences
Åbo Akademi University,
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Quoting "Dr. STEPHEN SIN-YIN, CHUI" <[log in to unmask]>:
> Dear Daniel
> Is the omit map for the model with and without the zinc ions
> possible to confirm
> its existence? I am curious. What is the resolution of dataset?
> Quoting Daniel Bonsor <[log in to unmask]>:
>> Hello again
>> I currently have some unexplained density in my structure. As you can
>> hopefully see from the images (see file), the density is dumbbell shaped.
>> Whatever it is, it is coordinated by Asp and Glu residues. To me it looks
>> like each lobe is a ring structure.
>> The crystallization condition was:
>> 6.5% PEG 8K, 10mM ZnSO4, 100mM sodium cacodylate pH 6.5, 100mM Am2SO4, 1%
>> glycerol, with 20% glycerol as cryo.
>> Protein was originally in 50mM Tris, 50mM NaCl pH 7.5.
>> I originally placed a single Zn at the center of each lobe. Though after
>> refmac, the Zn was displaced to one side. Two zincs in each
>> dumbbell may have
>> worked, but I am dubious about two zinc atoms being 4A apart and there is
>> still some unexplained density. Are there any possible cyclization reactions
>> of Tris, cacodylate or glycerol may have undergone to explain the
>> density? Or
>> is it simply a highly ordered water network? Or is there some other
>> Thanks in advance
> Dr. Stephen Sin-Yin Chui
> Research Assistant Professor,
> Department of Chemistry,
> The University of Hong Kong, Pokfulam Road,
> Hong Kong SAR, China.
> Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)