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| - | [[Image:246d.jpg|left|200px]] | |
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| + | ==STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE== |
| - | The line below this paragraph, containing "STRUCTURE_246d", creates the "Structure Box" on the page.
| + | <StructureSection load='246d' size='340' side='right'caption='[[246d]], [[Resolution|resolution]] 2.20Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <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> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</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> |
| - | {{STRUCTURE_246d| PDB=246d | SCENE= }}
| + | <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> |
| - | | + | </table> |
| - | '''STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Ban C]] |
| - | 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.
| + | [[Category: Ramakrishnan B]] |
| - | | + | [[Category: Sekharudu C]] |
| - | ==About this Structure==
| + | [[Category: Sundaralingam M]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=246D OCA]. | + | [[Category: Wahl MC]] |
| - | | + | |
| - | ==Reference== | + | |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/15299629 15299629]
| + | |
| - | [[Category: Ban, C.]]
| + | |
| - | [[Category: Ramakrishnan, B.]] | + | |
| - | [[Category: Sekharudu, C.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: Wahl, M C.]] | + | |
| - | [[Category: A-dna/rna]] | + | |
| - | [[Category: Double helix]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:22:42 2008''
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