PS: It may also help you to check the typical distances from zinc to
other elements - these data are collected here:
https://github.com/MonomerLibrary/monomers/blob/master/metals.json
as explained here:
https://github.com/MonomerLibrary/monomers/wiki/Dealing-with-metals#typical-interatomic-distances
Cheers,
Martin
On 12/03/2025 10:10, Martin Malý wrote:
Dear Shikha,
We recently released and published program MetalCoord which analyses
coordination geometry of metal sites and generate restraints to
stabilise refinement.
My suggestion would be to model there just a single zinc and refine
the structure. Then put that structure as an input to MetalCoord and
analyse zinc (monomer code ZN).
Then refine the structure with updated links which MetalCoord gives
you and with the restraints generated. After refinement, check the
atom distance and angle outliers.
When modelling of this tricky region became clearer, you can consider
to use anisotropic ADP just for the zinc.
There is a tutorial for MetalCoord available:
https://github.com/Lekaveh/MetalCoordAnalysis/blob/master/tutorial/tutorial.rst
Good luck! Please let me know how is it going.
Cheers,
Martin
On 12/03/2025 09:34, Shikha Gupta wrote:
Dear all,
I have a complex structure where zinc
metal ion is present in the active site (evidence from several PDBs).
However, despite multiple efforts, I am getting lot of positive
densities close to the metal ion (please see image attached). I have
also tried to place water or two zinc ions but that also doesn’t seem
to work. The last and overall best solution I came up with was by
positioning three zinc ions with combined occupancy of 1
(0.3+0.2+0.3). Although I still see positive densities around but
this is best I have achieved.
This was a soaked crystals, any suggestions on this. Is this the
right way to do this. The resolution of the structure is 1.7 angs.
Thanks,
Shikha
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