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<mailto: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 ________________________________ 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/
