Dear Julia, Thanks a lot for your input. I looked at your pdb/maps and yes, the context is similar, with the M2+ ion sitting near a His side chain, without further ligands nearby. Although this is not canonical chemistry for ions like these, I agree it must be some sort of water-metal ion adduct where waters might not be perfectly localized.
Cheers Talis On Mon, Mar 9, 2026 at 12:00 PM Julia Griese < [email protected]> wrote: > Hi Talis, > > > > I agree with everyone else, this has to be a metal ion. It is not strange > to see something like this, a metal ion with only one coordinating residue > on the protein surface, in a crystal that has been grown or soaked in a > high concentration of metal ions. A site like that is of course extremely > unlikely to be occupied in solution or to be physiologically relevant. > > > > I would also agree with Jon that it is most likely to be Cd because that > would be the strongest binder, but it depends on the relative amount of > each metal ion in your mixture. (See Irving-Williams series.) Since they’re > all at 5 mM in your case, it should be Cd. It will have loosely bound water > filling up the remaining coordination sites, hence the disk-like appearance > of the density. > > > > I have had a site exactly like that in a protein that I’ve worked with, > see e.g. PDB 4HR0, Mn(II) bound to His130. The site follows the > Irving-Williams series exactly. We dissected the origins of metal > specificity of the heterodinuclear Mn/Fe site of this protein, so I spent a > lot of time soaking the crystals with mixtures of different metal ions and > figuring out which ends up where using anomalous diffraction, therefore I > know exactly what is bound to all the sites, including the His130 site, > under which condition. Although not physiologically relevant, for me this > site was useful as an internal reference to distinguish good from bad > datasets. It is almost certainly overkill for you to go to that amount of > effort because it’s not a physiologically relevant site. I would go with > Cd. > > > > Best, > > > > Julia > > > > -- > > Dr. Julia Griese > > Associate Professor (Docent) > > Principal Investigator > > Department of Cell and Molecular Biology > > Uppsala University > > BMC, Box 596 > > SE-75124 Uppsala > > Sweden > > > > email: [email protected] > > phone: +46-(0)18-471 4982 > > Griese lab > <https://www.uu.se/en/department/cell-and-molecular-biology/research/structural-biology/griese-lab> > > > > > > *From: *CCP4 bulletin board <[email protected]> on behalf of Eleanor > Dodson <[email protected]> > *Date: *Monday, 9 March 2026 at 07:43 > *To: *[email protected] <[email protected]> > *Subject: *Re: [ccp4bb] Unusual density around His > > Anomalous peak height can give a clue.. any S atoms should also be marked > in the anom diff map and the relative peak heights might help decide? > > > > On Sun, 8 Mar 2026 at 22:39, Jon Cooper < > [email protected]> wrote: > > It must be cadmium which has atomic number 48 versus 27 for cobalt and 28 > for nickel. I would check that it could form a stoichiometric complex with > the protein at 5 mM with whatever protein concentration you used. It almost > certainly could. > > Best wishes, *Jon Cooper* (Emeritus at UCL) [email protected] > > Erratum and other hopefully useful things: https://crxp.org.uk > > > > Sent from Proton Mail <https://proton.me/mail/home> for Android. > > > > -------- Original Message -------- > > > On Sunday, 03/08/26 at 10:48 Greenstone talis < > [email protected]> wrote: > > Dear all, > > I have came across an unusual density feature in a structure refined at > 1.65 Å and would appreciate some opinions. > > There is a strong Fo–Fc positive density feature around the imidazole ring > of a His residue. The density looks broad and somewhat flat, almost like a > disk around the ring, rather than a compact peak.I initially thought it > might be a metal because the crystallization cocktail contains Cd²⁺, Mg²⁺, > Ni²⁺ and Co²⁺. Besides Fo-Fc results with one or another option, which of > course is relevant, what still confuses me is the absence of coordinating > ligands nearby. The density appears partially fused to the His side chain > rather than sitting clearly next to it. I am attaching three views of the > density from different angles (2Fo–Fc at 1 sigma, Fo–Fc at 3 sigma). > > Does this look like something people have seen before? Could it indicate > some PTM (for example oxidation or another chemical change), or is there > another explanation that I should consider? > > Any suggestions would be very helpful. > > (PROTEIN SOLUTION: TRIS AND NaCl) > > (CRYSTALLIZATION COCKTAIL: 0.005 M MgCl + 0.005 M NiCl + 0.005 M CoCl + > 0.005 M CdCl + 0.1 M HEPES pH 7.0, PEG 3350 + ETHYLENE GLYCOL) > > Thanks in advance. > > Talis > > > > > ------------------------------ > > 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 > > > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner > igen avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise > the sender and know the content is safe. > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. 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