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==Structure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at 1.4 A (Br1)==
==Structure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at 1.4 A (Br1)==
<StructureSection load='2r1s' size='340' side='right' caption='[[2r1s]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='2r1s' size='340' side='right'caption='[[2r1s]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2r1s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1S FirstGlance]. <br>
<table><tr><td colspan='2'>[[2r1s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1S FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.4&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2r20|2r20]], [[2r21|2r21]], [[2r22|2r22]]</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=2r1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1s OCA], [https://pdbe.org/2r1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1s RCSB], [https://www.ebi.ac.uk/pdbsum/2r1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1s ProSAT]</span></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=2r1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1s OCA], [http://pdbe.org/2r1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r1s RCSB], [http://www.ebi.ac.uk/pdbsum/2r1s PDBsum]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Metal ions play a key role in RNA folding and activity. Elucidating the rules that govern the binding of metal ions is therefore an essential step for better understanding the RNA functions. High-resolution data are a prerequisite for a detailed structural analysis of ion binding on RNA and, in particular, the observation of monovalent cations. Here, the high-resolution crystal structures of the tridecamer duplex r(GCGUUUGAAACGC) crystallized under different conditions provides new structural insights on ion binding on GAAA/UUU sequences that exhibit both unusual structural and functional properties in RNA. The present study extends the repertory of RNA ion binding sites in showing that the two first bases of UUU triplets constitute a specific site for sodium ions. A striking asymmetric pattern of metal ion binding in the two equivalent halves of the palindromic sequence demonstrates that sequence and its environment act together to bind metal ions. A highly ionophilic half that binds six metal ions allows, for the first time, the observation of a disodium cluster in RNA. The comparison of the equivalent halves of the duplex provides experimental evidences that ion binding correlates with structural alterations and groove contraction.
The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.,Timsit Y, Bombard S RNA. 2007 Dec;13(12):2098-107. Epub 2007 Oct 16. PMID:17940138<ref>PMID:17940138</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2r1s" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bombard, S]]
[[Category: Large Structures]]
[[Category: Timsit, Y]]
[[Category: Bombard S]]
[[Category: Asymmetry]]
[[Category: Timsit Y]]
[[Category: Electrostatic]]
[[Category: Monovalent cation]]
[[Category: Rna]]
[[Category: Structural plasticity]]

Latest revision as of 09:19, 21 February 2024

Structure of the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) at 1.4 A (Br1)

2r1s, resolution 1.40Å

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