Hi, I’m trying to model a N-O-S bond between a lysine side-chain and an oxidised cysteine (CSO) as described in https://www.nature.com/articles/s41467-024-48109-3
I’m facing two problems in Coot (v 0.9.8.3): Firstly, when I go >Replace residue and replace the cysteine with a CSO – Coot does not recognise the CSO as part of the peptide chain. I can manually (roughly) put it in place and Phenix will fix it during refinement, however this continues to be a problem for coot. Secondly, I have tried a couple of ways to model the NOS bond and none of them seem to work correctly. 1. I defined the link using JLigand, saved the cif file and the LINK record. I manually put this link in place in Coot, loaded the cif file into Phenix and it sort of worked, although the O-N bond length is too long and doesn’t match what is defined in the cif file (~1.99 Å vs 1.38 Å). Furthermore, after loading the cif file in coot, when I try to do a real space refine, it does not recognise the O-N link (or the CSO as part of the peptide chain as described above). 2. I defined the entire CSO-LYS as a ligand and generated cif restraints in Phenix using elBOW, loaded the pdb into Coot and placed into the density, merged with the pdb and tried to define “links” to the peptide backbone on both sides. As above, these bonds are not recognised by coot. After running through phenix, the planarity of the amide bonds is lost. To add to the complexity, there are two conformations of the N-O-S modification/linkage, so I also want to be able to model that. Any help would be greatly appreciated!! Thanks, Michelle --------------------------------------- Michelle Miller PhD Senior Research Officer Structural Biology E mille...@wehi.edu.au<mailto:mille...@wehi.edu.au> [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia www.wehi.edu.au<https://wehi.edu.au> Twitter<https://twitter.com/WEHI_research> | Facebook<https://www.facebook.com/WEHIresearch/> | Instagram<https://www.instagram.com/wehi_research> | Youtube<https://www.youtube.com/user/WEHImovies> | LinkedIn<https://www.linkedin.com/company/wehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. Private and confidential The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
