I think cacodilate is less likely because it's negatively charged as the
carboxy groups that surround the density.
I think it's Zn or it may be another (endogenous) metal ion like Ca. You
need to look at the coordination.
Maia
David Schuller wrote:
> The figures would be more helpful if you told us what each map contour
> represented, and at what contour level. I assume blue is 2fo-fc and
> green+red is fo-fc, positive and negative. It would be even more
> helpful to have the maps to turn over in 3D, but I understand you
> would probably be reluctant share that.
>
> The density looks much too strong to be mere water.
>
> Acidic surface residues may bind zinc. The metals might appear at
> multiple alternate locations, if the occupancies are less than 1.0.
> Synchrotron anomalous maps would be helpful in seeing Zinc, whose K
> edge is at 1.28 A.
>
> Multiple alternate locations are likely to show up at special symmetry
> positions. I have the impression this may be a special position in
> your map, but I can't be certain (2-fold axis?).
>
> Zinc and cacodylate may form cage complexes which can be bound
> between multiple surface acid resides (personal observation, not
> published). The complexes I have seen have one zinc at each pole with
> three cacodylates around the equator. Your density does not look
> especially similar to the complexes I have seen.
>
> Cacodylate also has a pretty good peak on anomalous maps, and since
> it's peak is at 1.04 A, anomalous maps at multiple wavelengths could
> distinguish between arsenic and zinc.
>
> On 04/29/10 17:38, Daniel Bonsor wrote:
>> 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 explanation?
>>
>> Thanks in advance
>>
>> Dan
>>
>
>
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