4xw7: Difference between revisions

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 ==Crystal structure of the ZMP riboswitch at 2.50 angstrom==
-<StructureSection load='4xw7' size='340' side='right' caption='[[4xw7]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='4xw7' size='340' side='right'caption='[[4xw7]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xw7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XW7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xw7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Schaalia_odontolytica Schaalia odontolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XW7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMZ:AMINOIMIDAZOLE+4-CARBOXAMIDE+RIBONUCLEOTIDE'>AMZ</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xwf|4xwf]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMZ:AMINOIMIDAZOLE+4-CARBOXAMIDE+RIBONUCLEOTIDE'>AMZ</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xw7 RCSB], [http://www.ebi.ac.uk/pdbsum/4xw7 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw7 OCA], [https://pdbe.org/4xw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xw7 RCSB], [https://www.ebi.ac.uk/pdbsum/4xw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xw7 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP. As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of N10-formyl-tetrahydrofolate, a key component of one-carbon metabolism. Here, we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 A. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the base, ribose sugar, and phosphate moieties of the ligand. Unique to nucleobase recognition by RNAs, the Z base is inner-sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over chemically similar compounds such as ATP/AMP.
-Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch.,Trausch JJ, Marcano-Velazquez JG, Matyjasik MM, Batey RT Chem Biol. 2015 Jul 23;22(7):829-37. doi: 10.1016/j.chembiol.2015.06.007. Epub, 2015 Jul 2. PMID:26144884<ref>PMID:26144884</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Batey, R T]]
+[[Category: Large Structures]]
-[[Category: Trausch, J J]]
+[[Category: Schaalia odontolytica]]
-[[Category: Aicar]]
+[[Category: Batey RT]]
-[[Category: Riboswitch]]
+[[Category: Trausch JJ]]
-[[Category: Rna]]
-[[Category: Zmp]]