[buster-discuss] Problem with hexacoordinated Mg2+

[Kikuti Carlos]

Hello guys,

This is a subject that keeps coming back from the ashes every few months or years, for different reasons… but I couldn’t find an answer in the Buster archives, so here it goes:

I’m refining a structure at 2.5 angstroms (2.2 with Staraniso) containing nucleotide + hexacoordinated Mg2+, but some of the side chains in the active site seem to be pushed away from the ion, and I am not sure the geometry of the phosphate moiety-Mg2+ bonds is correct . In this structure, Mg2+ is surrounded by 2 water molecules, 2 phosphate moieties from the nucleotide, two different residues from the myosin. Bond lengths are between 1.8 and 2.3 angstroms. This is a very common scenario in the lab, so your answer will potentially help improving many other future structures, especially the ones in lower resolution, and I’ve got a bunch of those.

 What I’ve tried already, using the Nov/22 version of Buster:

LINK records -> well… I thought CCP4/PDB were recommending this as the way to deal with all kinds of bonds (am I right?), but Buster/TNT/Gelly prefer to use LINK only for covalent bonds. My LINK records are filtered out from the beginning. Buster tells me to « manually describe coordination » , which is the main reason of this e-mail.
(This doesn’t look like the classic formatting/spacing issue as the error message would be different; and I also tried to invert the order of the ligands in the records, no success)

"good”(?) and old CONECT records -> nah… Buster just ignores them, the output doesn’t have any. I can’t restrain the bond lengths with this anyways.

"-Gelly file.dat" with NOTE_BUSTER_DISTANCE… -> from the log it seems this won’t work for HETATM, only for ATOM lines. Maybe there is something I should do in the .seq file?
  
I haven’t dealt with this kind of trouble for a while, so I am certainly missing something… could you please give me suggestions, or point me to some deeper source of information about this? 
(I’ve found an old presentation from Clemens that shows a hexacoordinated Mg2+. That made me salivate, but the protocol is not described)

Already thank you for your time reading this.

Best to you all,

---------------------------------------------------
Carlos KIKUTI, PhD
UMR144 - CNRS - Institut Curie
Pavillon Trouillet Rossignol

26 Rue d’Ulm - 75005 Paris, France
+33 6 82 87 62 76
carlos.kikuti at curie.fr 

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