Hello, can you get a good idea of the distance between the arginine sidechain nitrogen and the phosphorus? It should be less than 2 A for a covalent bond. A non-covalent complex will have an oxygen-nitrogen distance of about 2.8 A. If the Arg is phosphorylated, then this residue is already one of the RCSB standard ligands: https://www.rcsb.org/ligand/RPI So adding it should not be too hard in Coot and the other PDB entries with this residue (see link) should give you an idea of how the final PDB file should look. Apols for poetic spelling and hope some of this helps.
Sent from Yahoo Mail on Android On Sat, 27 Jul 2019 at 4:48, Anirudha Dutta<[email protected]> wrote: Hello everyoneFrom electron density, It looks like one of the arginines in my protein is post-translationally modified as phospho-arginine. How to make sure it's a real phospho-arginine, not an arginine interacting with phosphate or acetate ion? The resolution of the structure is 2.3 A. Can anybody helps me with step by step procedure to incorporate a phospho-arginine in my structure using COOT and if anything special need to be done during refinement in Phenix. Thanks and regardsSincerelyAnirudha Dutta To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
