On 17/03/2022 17:37, Mohd Syed Ahangar wrote:
I have been doing some protein crystal soaking with some covalently
binding fragments and in one structure I have got an extra density on
Cysteine but that density doesn't match with the expected fragment.
The fragment was in the form of iodide salt. when I fit the Iodine in
the density, it fitted fairly well than any other possible chemical
entity. From the density map it looks like something is covalently
bound to Cysteine.
Now my question is, can a sulphur atom of Cysteine have such an
interaction with Iodine.
No, they are both electronegative, C-S-I is not a thing.
The distance between S and Iodine is 2.76A in this case as shown in
the attached figure.
I would be grateful if someone can shed some light on this.
Your map (this figure) is a textbook example of a covalently linked atom
incorrectly refined with a non-bonded contact.
Paul.
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