Re: [ccp4bb] Cysteine-S-Iodine interaction

2022-03-31 Thread CRAIG A BINGMAN
: Re: [ccp4bb] Cysteine-S-Iodine interaction 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 wi

Re: [ccp4bb] Cysteine-S-Iodine interaction

2022-03-18 Thread Palm, Gottfried
Check the electron density (O, Cl, I ?) and the anomalous signal on your "iodine". Cysteine has an interesting chemistry and one is oxidation to the sulfenic acid, CSO, already mentioned. Probably, it is more common than we tend to expect and may be overlooked, because we don't look for it and

Re: [ccp4bb] Cysteine-S-Iodine interaction

2022-03-18 Thread Jose Artur Brito
Dear Modh, I agree with Paul, this is covalente modification of Cys. I would try cysteine persulfide (CSS), and cysteine sulfenic acid (CSO). In COOT, center on this cysteine, and then do: Calculate -> Modelling -> Replace residue; write CSS (or CSO), save the coordinates and refine. HTH,

Re: [ccp4bb] Cysteine-S-Iodine interaction

2022-03-18 Thread Michał Taube
Hi, it may be oxidized cysteine. Look here: https://www.researchgate.net/publication/44656220_Protein_S-thiolation_by_glutathionylspermidine_Gsp_The_role_of_Escherichia_coli_Gsp_synthetASEamidase_in_redox_regulation and here: Trundle D, Cunningham LW. Iodine oxidation of the sulfhydryl groups of

Re: [ccp4bb] Cysteine-S-Iodine interaction

2022-03-18 Thread Paul Emsley
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