Dear All,
thanks for the plug Harry! I would say that fluoromagnesates are rather
flexible in terms of their geometry, as opposed to the aluminium and
beryllium companions that are strictly octahedral and tetrahedral
respectively. MgF3- is mostly observed as a planar trigonal bipyramidal
species but has also been observed in octahedral, and interestingly, as
a tetrahedral MgF42- species - most famously in the SERCA P-type ATPase
(see https://doi.org/10.1038/nature02981)
So, as others have said, I would go with what the density is showing
you! Best wishes, Matt
On 03/02/2026 10:21, CCP4BB wrote:
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
<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
<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
<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>
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