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 Sun, Apr 4, 2021 at 10:27 AM Debanu <deb...@alumni.rutgers.edu> wrote: > 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/
