Exactly. Deviation from usual geomatry usually means some particle being transferred and reaction mechanism being captured... --- Michal Navrátil, PhD
út 3. 2. 2026 v 10:22 odesílatel CCP4BB < [email protected]> napsal: > This > > https://www.sciencedirect.com/science/article/pii/S0969212624002703 > > Suggests that MgF3- (sorry about the lack of super- and subscripts) should > be distorted trigonal bipyramidal. > > Given the disparity in the Mg-O distances (2.0 and ~3.0Å) I'd expect the > MgF3 fragment to be non-planar, because the interactions between the Mg and > O atoms are clearly different. > > Harry > > On 3 Feb 2026, at 09:10, Martin Malý < > [email protected]> wrote: > > Dear Friday, > > This looks interesting. I would suggest to try our program MetalCoord > which is in CCP4 to get information about possible geometry and > coordination (and restraints - we provide in Refmac/Servalcat as well as in > Phenix.refine syntax, see our tutorial). In the related paper, we reported > something analogous - unusual geometry for aluminium fluoride AlF3. I would > be interested if the program helps in your case. Feel free to send me the > coordinates offlist. > > The latest AceDRG also support stereochemistry dictionary generation when > accounting for a chemical context around a metal (option --metalPDB= ). > It's available in CCP4i2 or using the command line: > acedrg -c MGF.cif -r MGF --metalPDB=structure.pdb -o acedrg_MGF > > Cheers, > Martin > > I think this topic is relevant for any of the CCP4BB or Phenix mailing > list. Users often combine software (and related information) from different > suites and it's completely fine. > > > On 03/02/2026 08:09, Bruno KLAHOLZ wrote: > > > > Dear Friday, > > > > indeed, when looking at the image below it seems it cannot be planar here: > look at the angle between the water molecule on the left and the oxygen > atom of the phosphate on the right: it is clearly less than 180°. A planar > transition state would imply a co-linear arrangement normally. > > > > Best, > > > > Bruno > > > > > > > > ------------------------------- > > > > *From:* CCP4 bulletin board <[email protected]> > <[email protected]> *On Behalf Of *Jeroen Mesters > *Sent:* mardi 3 février 2026 08:41 > *To:* [email protected] > *Subject:* Re: [ccp4bb] MgF3 not coplanar > > > > Hi, > > > > I agree with Doeke, you are not the first to observe a deviation from > coplanarity. > > > > In https://doi.org/10.1016/S1074-5521(02)00112-6 you can find the > following statement: > > > > "Nevertheless, examples have been described of magnesium adopting > penta-covalent bonding with distorted trigonal bipyramidal geometry [23]." > > > > Reference/Review 23 is about magnesium compounds/constellations in > crystallography: https://doi.org/10.1016/0022-328X(94)87036-5 > > > > A comparison between refined models with and without a coplanar constraint > on the MgF3- is a first step to try and resolve the issue. > > > > Do not discard the „deviation from coplanarity" possibility *a priori* > > > > Cheers, > > > > Jeroen > > __ > > Dr. *math. et dis. nat.* Jeroen R. Mesters > Biological Safety Officer (BBS) > Deputy, Lecturer, Program Coordinator Infection Biology > Visiting Professorship in Biophysics - University South Bohemia > > > University of Lübeck > Center for Structural and Cell Biology in Medicine > Institute of Biochemistry > Ratzeburger Allee 160 > 23562 Lübeck > > Tel +49 451 3101 3105 > https://orcid.org/0000-0001-8532-6699 > > > > > > > > *From:* CCP4 bulletin board <[email protected]> > <[email protected]> *On Behalf Of *Hekstra, Doeke Romke > *Sent:* mardi 3 février 2026 04:08 > *To:* [email protected] > *Subject:* Re: [ccp4bb] MgF3 not coplanar > > > > Hi Friday, > > > > Perhaps nature disagrees with you! It may be that that water would like to > turn this into something more tetrahedral :) > > > > Best, Doeke > > > > *From:* CCP4 bulletin board <[email protected]> *On Behalf Of *Pavel > Afonine > *Sent:* Monday, February 2, 2026 9:44 PM > *To:* [email protected] > *Subject:* Re: [ccp4bb] MgF3 not coplanar > > > > Hello Friday, > > The library file for MGF indeed does not define a plane. Whether a plane > should be defined, I don’t know—that’s beyond my chemistry curriculum. The > file is: > > phenix/modules/chem_data/geostd/m/data_MGF.cif > > phenix.refine allows you to force any selected set of atoms to be planar. > Please consult the documentation for how-tos. If you have additional > questions, I’ll be happy to answer offlist or on the Phenix mailing list > (yes, this is not a Phenix mailing list!). > > Good luck! > Pavel > > > > > > On Mon, Feb 2, 2026 at 6:31 PM Friday < > [email protected]> wrote: > > Dear community, > > > > I recently solved a structure that uses MgF3 to mimic the 3rd phosphate of > GTP. The structure was refined with Phenix. The MgF3 is supposed to be > coplanar, however, it was slightly off. How do I force it to be coplanar? > Thanks! > > > > Friday > > > > <image002.png> > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=CnPMyOxiRar030kKzDeal7HF-X2g9kdkcaqJyw8LNTxdDfiXbtwOBEzaZ3bNHK5Z&s=H-yN2BntW8DyM59EuIqWMOyf2TJ1dDP1CMloX59CgQE&e=> > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=CnPMyOxiRar030kKzDeal7HF-X2g9kdkcaqJyw8LNTxdDfiXbtwOBEzaZ3bNHK5Z&s=H-yN2BntW8DyM59EuIqWMOyf2TJ1dDP1CMloX59CgQE&e=> > > > ------------------------------ > > 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 > ######################################################################## 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/
