246d

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(New page: 200px<br /><applet load="246d" size="350" color="white" frame="true" align="right" spinBox="true" caption="246d, resolution 2.200&Aring;" /> '''STRUCTURE OF THE PU...)
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[[Image:246d.jpg|left|200px]]<br /><applet load="246d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="246d, resolution 2.200&Aring;" />
 
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'''STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE'''<br />
 
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==Overview==
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==STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE==
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The crystal structure of the purine-pyrimidine alternating octameric RNA, helix, r(GUAUAUA)d(C), carrying a 3'-terminal deoxycytidine residue, has, been determined at 2.2 A resolution. The molecule crystallizes in the, rhombohedral space group R3 (hexagonal cell constants: a = b = 43.07,c =, 59.36 A;alpha = beta = 90,gamma = 120 degrees )with one duplex in an, asymmetric unit. The structure was solved by molecular replacement and, refined with 83 and 2/3 solvent molecules and 2/3 sodium ions to a final R, factor of 15.6% using 1775 reflections (86%). The duplexes are, approximately linear, their global helix axes are inclined by 10 degrees, with respect to the 3(2)-screw axes, and they are stacked on top of each, other in a head-to-tail fashion. The twist between the junction base pairs, of the stacked duplexes is negligible resulting in a discontinuity of the, helix backbones and grooves. The sodium ions on the threefold axis play a, significant role in the organization of the packing network. The helical, parameters, particularly the twist and the roll, of this alternating, sequence are in accord with Calladine's rules. Almost all the 2'-hydroxyl, groups are involved in specific hydrogen-bonding interactions, either, directly to the sugar ring oxygens O4' on the 3' side, or, through water, bridges, to the sugars, phosphates, or bases. This hydrogen bonding of the, 2'-hydroxyl groups restrains the conformation of the sugar-phosphate, backbone and the glycosidic torsion angles of this RNA fragment. The lack, of intermolecular packing contacts in the grooves provides a clear picture, of the groove solvation.
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<StructureSection load='246d' size='340' side='right'caption='[[246d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[246d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=246D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=246D FirstGlance]. <br>
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246D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=246D OCA].
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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]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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==Reference==
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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=246d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=246d OCA], [https://pdbe.org/246d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=246d RCSB], [https://www.ebi.ac.uk/pdbsum/246d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=246d ProSAT]</span></td></tr>
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Structure of the purine-pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue., Wahl MC, Ban C, Sekharudu C, Ramakrishnan B, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):655-67. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15299629 15299629]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Ban, C.]]
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</StructureSection>
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[[Category: Ramakrishnan, B.]]
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[[Category: Large Structures]]
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[[Category: Sekharudu, C.]]
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[[Category: Ban C]]
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[[Category: Sundaralingam, M.]]
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[[Category: Ramakrishnan B]]
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[[Category: Wahl, M.C.]]
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[[Category: Sekharudu C]]
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[[Category: NA]]
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[[Category: Sundaralingam M]]
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[[Category: a-dna/rna]]
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[[Category: Wahl MC]]
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[[Category: double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:48:55 2008''
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Current revision

STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE

PDB ID 246d

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