Re: [ccp4bb] Cysteine-S-Iodine interaction
I’m late to the party here, but there are (at least) 59 instances of a C-S-I fragment in the CCDC. Flipping through the first third of the list, GIGBED (triphenylmethyl-iodo-sulfane) seems somewhat close. The S-I bond is 2.41Å and the C-S-I bond angle is 105.4 degrees. There may be better ones deeper in the list, but that’s someone else’s project to find. (R.Minkwitz, H.Preut, J.Sawatzki, Zeitschrift fur Naturforschung,B:Chemical Sciences, 1988, 43, 399) From: CCP4 bulletin board on behalf of Paul Emsley Date: Friday, March 18, 2022 at 3:05 AM To: CCP4BB@JISCMAIL.AC.UK Subject: 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 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. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Cysteine-S-Iodine interaction
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 because it is further oxidized to the sulfonic acid during purification. Even more unexpected is the sulfenylchloride, R-S-Cl. A redox sensor we worked on has a reactive cysteine which is oxidized (eventually to a disulfide) by hydrogenperoxide, most likely the mechanism goes via H2O2 + Cl- --> HOCl, RSH + HOCl --> RSCl, RSCl + RSH --> RSSR. Thus, sulfenylchloride has a physiological role, why not sulfenyliodide. I am not sure, if it is long lived enough to be ever crystallized, though. Greetings Gottfried Am Freitag, den 18-03-2022 um 09:04 schrieb 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 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. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Cysteine-S-Iodine interaction
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, Jose --- * Jose Artur Brito, PhD * * * * Membrane Protein Crystallography Laboratory * * Instituto de Tecnologia Quimica e Biologica Antonio Xavier * * Oeiras - PORTUGAL * * * * Phone - +351 214 469 760 (office) / +351 962 452 179 (mobile) * * * * Website - http://www.itqb.unl.pt/researchers/jbrito * -- Date:Thu, 17 Mar 2022 17:37:17 + From:Mohd Syed Ahangar Subject: Cysteine-S-Iodine interaction Hi CCP4BB members. 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. 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. Thank you in advance. -- Dr. Mohd Syed Ahanger, Faculty of Biological Sciences, University of Leeds, Leeds, UK. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Cysteine-S-Iodine interaction
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 creatine kinase. Biochemistry. 1969;8:1919–1925. Best Michal czw., 17 mar 2022 o 18:37 Mohd Syed Ahangar napisał(a): > Hi CCP4BB members. > > 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. 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. > > Thank you in advance. > -- > > Dr. Mohd Syed Ahanger, > > Faculty of Biological Sciences, > > University of Leeds, Leeds, UK. > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
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 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. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
