439d: Difference between revisions

Line 1:

~~{{STRUCTURE_439d| PDB=439d | SCENE= }}~~

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

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

~~{{ABSTRACT_PUBMED_11173467}}~~

== Structural highlights ==

<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=439D FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</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=439d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=439d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=439d RCSB], [http://www.ebi.ac.uk/pdbsum/439d PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

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'.

~~==About this~~ Structure==

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>

~~[[439d]] is a~~ 2 ~~chain structure~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin~~/~~ocashort?id=439D OCA].~~

[[Category: Betzel, C.]]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: Erdmann, V A.]]

</div>

[[Category: Lorenz, S.]]

== References ==

[[Category: Perbandt, M.]]

[[Category: Vallazza, M.]]

__TOC__

</StructureSection>

[[Category: Betzel, C]]

[[Category: Erdmann, V A]]

[[Category: Lorenz, S]]

[[Category: Perbandt, M]]

[[Category: Vallazza, M]]

[[Category: A-rna]]

[[Category: Fragment of 5s rrna]]

[[Category: Rna]]

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@@ Line 1: / Line 1: @@
-{{STRUCTURE_439d|  PDB=439d  |  SCENE=  }}
+==5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'==
-===5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'===
+<StructureSection load='439d' size='340' side='right' caption='[[439d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-{{ABSTRACT_PUBMED_11173467}}
+== Structural highlights ==
+<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=439D FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</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=439d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=439d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=439d RCSB], [http://www.ebi.ac.uk/pdbsum/439d PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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'.
-==About this Structure==
+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>
-[[439d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=439D OCA].
-[[Category: Betzel, C.]]
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Erdmann, V A.]]
+</div>
-[[Category: Lorenz, S.]]
+== References ==
-[[Category: Perbandt, M.]]
+<references/>
-[[Category: Vallazza, M.]]
+__TOC__
+</StructureSection>
+[[Category: Betzel, C]]
+[[Category: Erdmann, V A]]
+[[Category: Lorenz, S]]
+[[Category: Perbandt, M]]
+[[Category: Vallazza, M]]
 [[Category: A-rna]]
 [[Category: Fragment of 5s rrna]]
 [[Category: Rna]]