439d

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[[Image:439d.gif|left|200px]]
 
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{{Structure
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==5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'==
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|PDB= 439d |SIZE=350|CAPTION= <scene name='initialview01'>439d</scene>, resolution 1.6&Aring;
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<StructureSection load='439d' size='340' side='right'caption='[[439d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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<table><tr><td colspan='2'>[[439d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=439D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=439D FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene></td></tr>
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|DOMAIN=
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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=439d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=439d OCA], [https://pdbe.org/439d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=439d RCSB], [https://www.ebi.ac.uk/pdbsum/439d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=439d ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=439d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=439d OCA], [http://www.ebi.ac.uk/pdbsum/439d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=439d RCSB]</span>
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<div style="background-color:#fffaf0;">
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}}
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== Publication Abstract from PubMed ==
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'''5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3''''
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==Overview==
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The structure of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) has been determined at 1.6 A resolution and refined to a final R factor of 18.3% (R(free) = 24.1%). The sequence of the RNA fragment resembles domain E of Thermus flavus 5S rRNA. A previously undescribed wobble-like G.C base-pair formation is found. Owing to the observed hydrogen-bond network, it is proposed that the cytosine is protonated at position N3. The unusual base-pair formation is presumably strained by intermolecular interactions. In this context, crystal packing and particular intermolecular contacts may have direct influence on the three-dimensional structure. Furthermore, this structure includes two G.U wobble base pairs in tandem conformation, with the purines forming a so-called 'cross-strand G stack'.
The structure of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) has been determined at 1.6 A resolution and refined to a final R factor of 18.3% (R(free) = 24.1%). The sequence of the RNA fragment resembles domain E of Thermus flavus 5S rRNA. A previously undescribed wobble-like G.C base-pair formation is found. Owing to the observed hydrogen-bond network, it is proposed that the cytosine is protonated at position N3. The unusual base-pair formation is presumably strained by intermolecular interactions. In this context, crystal packing and particular intermolecular contacts may have direct influence on the three-dimensional structure. Furthermore, this structure includes two G.U wobble base pairs in tandem conformation, with the purines forming a so-called 'cross-strand G stack'.
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==About this Structure==
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Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution.,Perbandt M, Vallazza M, Lippmann C, Betzel C, Erdmann VA Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):219-24. PMID:11173467<ref>PMID:11173467</ref>
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439D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=439D OCA].
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==Reference==
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Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution., Perbandt M, Vallazza M, Lippmann C, Betzel C, Erdmann VA, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):219-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11173467 11173467]
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[[Category: Protein complex]]
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[[Category: Betzel, C.]]
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[[Category: Erdmann, V A.]]
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[[Category: Lorenz, S.]]
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[[Category: Perbandt, M.]]
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[[Category: Vallazza, M.]]
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[[Category: a-rna]]
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[[Category: fragment of 5s rrna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:13 2008''
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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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<div class="pdbe-citations 439d" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Betzel C]]
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[[Category: Erdmann VA]]
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[[Category: Lorenz S]]
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[[Category: Perbandt M]]
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[[Category: Vallazza M]]

Current revision

5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'

PDB ID 439d

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