2lps

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==Molecular dynamics re-refinement of domain 5 of the yeast ai5(gamma) group II intron==
==Molecular dynamics re-refinement of domain 5 of the yeast ai5(gamma) group II intron==
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<StructureSection load='2lps' size='340' side='right' caption='[[2lps]], [[NMR_Ensembles_of_Models | 5 NMR models]]' scene=''>
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<StructureSection load='2lps' size='340' side='right'caption='[[2lps]]' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2lps]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LPS FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2lps]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LPS FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1r2p|1r2p]], [[1kxk|1kxk]], [[2lpt|2lpt]]</td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lps OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lps RCSB], [http://www.ebi.ac.uk/pdbsum/2lps PDBsum]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lps OCA], [https://pdbe.org/2lps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lps RCSB], [https://www.ebi.ac.uk/pdbsum/2lps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lps ProSAT]</span></td></tr>
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<table>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site.
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Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.,Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM Nat Struct Mol Biol. 2004 Feb;11(2):187-92. Epub 2004 Jan 25. PMID:14745440<ref>PMID:14745440</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Davis, D R.]]
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[[Category: Large Structures]]
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[[Category: Henriksen, N M.]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: III, T E.Cheatham.]]
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[[Category: Cheatham III TE]]
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[[Category: Bulge]]
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[[Category: Davis DR]]
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[[Category: Rna]]
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[[Category: Henriksen NM]]
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[[Category: Tetraloop]]
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Current revision

Molecular dynamics re-refinement of domain 5 of the yeast ai5(gamma) group II intron

PDB ID 2lps

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