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<div dir="auto" style="word-wrap:break-word; line-break:after-white-space" class="">Hello guys,
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<div class="">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:</div>
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<div class="">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.</div><div class=""><br class=""></div><div class=""> What I’ve tried already, using the Nov/22 version of Buster:</div>
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<div class="">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.</div>
(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)<br class="">
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<div class="">"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.</div><div class=""><br class=""></div><div class="">
<div class="">"-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?</div>
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<div class="">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? </div><div class="">(I’ve found an old presentation from Clemens that shows a hexacoordinated Mg2+. That made me salivate, but the protocol is not described)</div><div class=""><br class=""></div><div class="">Already thank you for your time reading this.</div><div class=""><br class=""></div><div class="">Best to you all,</div><div class=""><br class=""></div><div class="">
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<div>---------------------------------------------------<br class="">
Carlos KIKUTI, PhD<br class="">
UMR144 - CNRS - Institut Curie</div>
<div>Pavillon Trouillet Rossignol<span class="Apple-tab-span" style="white-space:pre">
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26 Rue d’Ulm - 75005 Paris, France<br class="">
+33 6 82 87 62 76<br class="">
<a href="mailto:carlos.kikuti@curie.fr" class="">carlos.kikuti@curie.fr</a><span class="Apple-tab-span" style="white-space:pre"> </span>
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