The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so it’s probably mainly water molecules. Perhaps partially replaced by PEG to explain the density between them (i.e. water molecules in most copies of the protein and PEG in some other copies). I’ve seen horse-shoe shaped PEG in a high-res structure before, PEGs in several confirmations might explain a circle. Practically speaking, I’d first model five waters and see if they refine well.
Mark > On 22 Mar 2021, at 14:58, Sam Tang <samtys0...@gmail.com> wrote: > > Hello fellow colleagues > > Hope you are all well while the pandemics persists. I just wonder if anyone > may have an idea what this density (looking like a pentagon) might be. The > data was collected to 1.8 A and crystal was grown in Bis-tris + PEG3350. > Imidazole residual? Nucleotide (the protein itself is nucleotide-binding, but > shouldn't be at this particular site)? > > https://drive.google.com/file/d/1L9UBFmW72P214itM2HJR_DVy3FaA6FEZ/view?usp=sharing > > <https://drive.google.com/file/d/1L9UBFmW72P214itM2HJR_DVy3FaA6FEZ/view?usp=sharing> > > Thanks! > > BRS > > Sam > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
