Hi, This may be of interest in this discussion (the abstract is enlightening in itself):
"Water polygons in high‐resolution protein crystal structures" Jonas Lee, Sung‐Hou Kim https://pubmed.ncbi.nlm.nih.gov/19551896/ Download software here (you can analyze input pdb file to look at water polygon structures): https://sourceforge.net/projects/pdbwaterpolygon/ Thanks, Debanu On Tue, Mar 23, 2021 at 2:15 AM Barone, Matthias <bar...@fmp-berlin.de> wrote: > can confirm jon´s comment. I find these in virtually every high-res > structure. some of them wobble a bit given the AA close by, such as Arg. > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jon > Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> > *Sent:* Monday, March 22, 2021 5:38:40 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] unknown density > > Definitely water pentamer, no doubt at all ;-0 > Cheers, Jon.C. > > Sent from ProtonMail mobile > > > > -------- Original Message -------- > On 22 Mar 2021, 14:16, Mark J. van Raaij < mjvanra...@cnb.csic.es> wrote: > > > 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 > > 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 > > > ######################################################################## 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/
