Dear Arpita, The hydrogens on phosphate, just like sodium and potassium, will come off the oxygens in water. To be more explicit, you don't have mono- or di-hydrogen phosphate in water (except transiently), you just have phosphate, depending somewhat on the pH of course. At 2.5 Angstrom resolution, there is no way to 'see' hydrogens with X-rays. Depending on the wavelength you used for your data collection, you could try doing an anomalous map and see if you have any anomalous signal at this position, which may help in identifying what the density is. Best of luck, tom
________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Arpita Goswami <bt.arp...@gmail.com> Sent: Sunday, December 17, 2023 9:46 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Query on density fitting to phosphate You don't often get email from bt.arp...@gmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Dear All, Hope you all are doing well. The density in the image (in link below) is fitted with PO4 ion, although the crystallization condition has both mono and dihydrogen phosphate which is not fitting without hydrogen. But the resolution is 2.5 A, so hydrogen may not be put in, or is there any way to do so? Otherwise placing water is the final option. https://i.postimg.cc/4N7q2K0p/Screenshot-from-2023-12-17-16-07-07.png Also the density is quite close to Aspartate, so PO4 may not be right. Can it be dihydrogen phosphate as two positively charged residues (Specially the lysine) are also nearby to neutralize positive charge? Other ions in the crystallization condition are Cl-, K+ and Na+. These are not put as both aspartate and lysine are at comparable distances from the density. The pH is 6.2 in which dihydrogen phosphate is reported to interact with aspartate (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855859/). Waiting eagerly for your reply. -- Thanks and Merry Christmas in advance. Best Regards, Arpita ________________________________ 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/
