Hi, Thank you all for the replies.
As suggested, this is the residual positive difference density after putting water and refinement in coot-refmac: https://i.postimg.cc/DfbrbDZm/Screenshot-from-2023-12-19-16-39-38.png Does this look like any of the three phosphate ions? Two sides are similar, while one side is a little longer than others. H2PO4- has single negative charged Oxygen. The alternate conformation of the said arginine may not be possible as it is situated quite far from aspartate. As suggested both H2PO4- and HPO42- should dissociate to phosphate ions. Is it possible some H2PO4- will remain undissociated at pH 6.2 at low temperature like 4 degree centigrade (crystallization condition)? The pKa of H2PO4- dissociation is 7.2. Thank you for the suggestion of an anomalous map. We used 1.5412 A wavelength for data collection. So for an anomalous map for Phosphorus we do not have the data for now. I tried sodium and potassium ions. Sodium gives residual positive difference density as seen in water, for potassium also likewise. Also presence of lysine at close distance is not helpful for them. Waiting eagerly for your reply. -- Thank you. Best Regards, Arpita On Mon, Dec 18, 2023 at 7:01 AM Joel Tyndall <joel.tynd...@otago.ac.nz> wrote: > Have you tried sodium? > > > > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *Arpita > Goswami > *Sent:* Sunday, December 17, 2023 11:47 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Query on density fitting to phosphate > > > > 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/
