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]> 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]> 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 >> >> >> 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/
