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419d

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OCTAMER 5'-R(GPUPAPUPAPCPA)-D(PC)-3' WITH SIX WATSON-CRICK BASE-PAIRS AND TWO 3' OVERHANG RESIDUES

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Retrieved from "http://52.214.119.220/wiki/index.php/419d"

Categories: Large Structures | Biswas R | Mitra SM | Shi K | Sundaralingam M

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-[[Image:419d.gif|left|200px]]<br /><applet load="419d" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="419d, resolution 2.200&Aring;" />
-'''OCTAMER 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' WITH SIX WATSON-CRICK BASE-PAIRS AND TWO 3' OVERHANG RESIDUES'''<br />
-==Overview==
+==OCTAMER 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' WITH SIX WATSON-CRICK BASE-PAIRS AND TWO 3' OVERHANG RESIDUES==
-The crystal structure of an alternating RNA octamer, r(guauaca)dC (RNA, bases are in lower case while the only DNA base is in upper case), with, two 3' overhang residues one of them a terminal deoxycytosine and the, other a ribose adenine, has been determined at 2.2 A resolution. The, refined structure has an Rwork 18.6% and Rfree 26.8%. There are two, independent duplexes (molecules I and II) in the asymmetric unit cell, a =, 24.95, b = 45.25 and c = 73.67 A, with space group P2(1)2(1)2(1). Instead, of forming a blunt end duplex with two a+.c mispairs and six Watson-Crick, base-pairs, the strands in the duplex slide towards the 3' direction, forming a two-base overhang (radC) and a six Watson-Crick base-paired, duplex. The duplexes are bent (molecule I, 20 degrees; molecule II, 25, degrees) and stack head-to-head to form a right-handed superhelix. The, overhang residues are looped out and the penultimate adenines of the two, residues at the top end (A15) are anti and at the bottom (A7) end are syn., The syn adenine bases form minor groove A*(G.C) base triples with, C8-H...N2 hydrogen bonds. The anti adenine in molecule II also forms a, triple and a different C2-H...N3 hydrogen bond, while the other anti, adenine in molecule I does not, it stacks on the looped out overhang base, dC. The 3' terminal deoxycytosines form two stacked hemiprotonated trans, d(C.C)+ base-pairs and the pseudo dyad related molecules form four, consecutive deoxyribose and ribose zipper hydrogen bonds in the minor, groove.
+<StructureSection load='419d' size='340' side='right'caption='[[419d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[419d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=419D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=419D FirstGlance]. <br>
-D is a [http://en.wikipedia.org/wiki/Protein_complex 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=419D OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</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=419d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=419d OCA], [https://pdbe.org/419d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=419d RCSB], [https://www.ebi.ac.uk/pdbsum/419d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=419d ProSAT]</span></td></tr>
-==Reference==
+</table>
-The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues., Shi K, Biswas R, Mitra SN, Sundaralingam M, J Mol Biol. 2000 May 26;299(1):113-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10860726 10860726]
+__TOC__
-[[Category: Protein complex]]
+</StructureSection>
-[[Category: Biswas, R.]]
+[[Category: Large Structures]]
-[[Category: Mitra, S.M.]]
+[[Category: Biswas R]]
-[[Category: Shi, K.]]
+[[Category: Mitra SM]]
-[[Category: Sundaralingam, M.]]
+[[Category: Shi K]]
-[[Category: highly bent rna]]
+[[Category: Sundaralingam M]]
-[[Category: superhelices]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:42:43 2008''

419d

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OCTAMER 5'-R(GPUPAPUPAPCPA)-D(PC)-3' WITH SIX WATSON-CRICK BASE-PAIRS AND TWO 3' OVERHANG RESIDUES

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