Hello, could this be a case of the ZN not being shifted one place to the left in the PDB file to give it the right scattering factor ? ? The progs are pushing neighbouring atoms into the Zn density to account for its scattering power ? ? Maybe these problems don't happen any more.
Sent from ProtonMail mobile -------- Original Message -------- On 11 Apr 2022, 15:55, Martin Moche wrote: > Dear colleagues, > > We are refining a structure where an acetate ion (ACT) binds a zinc ion, Zn+2 > (ZN), using an excellent quality 1.38Å dataset, however the acetate oxygen > ends up too close (1.2Å) to the ZN during restrained refinement in refmac5? > Moreover, the ACT ion gets “deformed” so that the acetate oxygen-carbon bond > gets extended into 1.4Å? > > When doing COOT sphere refinement, the acetate ion moves on top of the ZN? > like the ZN was not there? And we think this would happen also in refmac5, if > the electron density were not holding acetate ion back from entering the zinc > site. We guess on a “tug of war” between ZN site attraction for acetate > oxygen, and electron density for other three acetate atoms, is deforming the > acetate ion. Why is the acetate ion not aware of the ZN in COOT? and refmac5… > > In the attached image, we removed the deformed acetate ion from refinement > resulting in the green difference density contoured at 5σ. The deformed > acetate from previous refinements (gold color carbons) has a carbon-oxygen > bond of 1.4Å and an oxygen-zinc distance of 1.2Å. The oxygen-zinc distance is > typically around 1.8Å for previous acetate ions (magenta carbons) modeled in > other PDB entries of the same enzyme. > > To get more reasonable refinement we manually attempted to add LINK (and > LINKR) restraints in the PDB file for the oxygen-zinc bond but that had no > impact on refmac5 and COOT refinement? although notified in the refmac5 > logfiles (attached). > > COOT is intended to parse LINK records and are not using nonbonded restraints > (1). We share our LINK records here for review. > > LINK ZN ZN A 625 OE1 GLU A 318 1555 1555 2.060 > > LINK ZN ZN A 625 OE2 GLU A 318 1555 1555 2.060 > > LINK O ACT A 623 ZN ZN A 625 1555 1555 2.060 > > LINKR O ACT A 623 ZN ZN A 625 1555 1555ACT-ZN > > LINKR ZN ZN A 625 NE2 HIS A 299 ZN-HISNE > > LINKR ZN ZN A 625 NE2 HIS A 295 ZN-HISNE > > We tried with one LINK or LINKR row or with both present in PDB (as above) > and used various checkboxes under “Advanced options” (pictured) under > Refinement-Refmac5 > Inputs > Restraints > > Metal coordination vary with oxidation state and despite AceDRG (2) and > recent CCP4 developments (3) we are now struggling with Zinc and acetate ion > in our refinement. > > Maybe we have run into a BUG? or how should we proceed? > > Best regards, > > Martin > > P.S. > > Also, in phenix.refine the acetate ion moves too close to the ZN? And one if > the zinc coordinated water molecules left its electron density and moved > towards the ZN..? > > D.S. > > 1. Casanal A, Lohkamp B, Emsley P. Current developments in Coot for > macromolecular model building of Electron Cryo-microscopy and > Crystallographic Data. Protein Sci. 2020;29(4):1069-78.doi:10.1002/pro.3791. > > 2. Nicholls RA, Joosten RP, Long F, Wojdyr M, Lebedev A, Krissinel E, > Catapano L, Fischer M, Emsley P, Murshudov GN. Modelling covalent linkages in > CCP4. Acta Crystallogr D Struct Biol. 2021;77(Pt > 6):712-26.doi:10.1107/S2059798321001753. > > 3. Nicholls RA, Wojdyr M, Joosten RP, Catapano L, Long F, Fischer M, Emsley > P, Murshudov GN. The missing link: covalent linkages in structural models. > Acta Crystallogr D Struct Biol. 2021;77(Pt > 6):727-45.doi:10.1107/S2059798321003934. > > [Head of Macromolecular X-ray Crystallography](https://ki.se/en/mbb/psf-mx) | > [Protein Science Facility](https://ki.se/en/mbb/protein-science-facility) > > [Medical Biochemistry and > Biophysics](https://ki.se/en/mbb/department-of-medical-biochemistry-and-biophysics) > > 171 65 Solna | Solnavägen 9 > > +46 8 524 868 43 | +46 73 322 93 27 > > [email protected] | [ki.se](https://ki.se/) > > ______________________________________ > > Karolinska Institutet – a medical university > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI > kommer att behandla dina personuppgifter. [Här finns information om hur KI > behandlar personuppgifter](https://ki.se/medarbetare/integritetsskyddspolicy). > > Sending email to Karolinska Institutet (KI) will result in KI processing your > personal data. [You can read more about KI’s processing of personal data > here](https://ki.se/en/staff/data-protection-policy). > > --------------------------------------------------------------- > > 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/
