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| - | [[Image:2ao5.gif|left|200px]] | |
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| - | <!--
| + | ==Crystal structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G-U base pairs== |
| - | The line below this paragraph, containing "STRUCTURE_2ao5", creates the "Structure Box" on the page.
| + | <StructureSection load='2ao5' size='340' side='right'caption='[[2ao5]], [[Resolution|resolution]] 2.10Å' 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'>[[2ao5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AO5 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]] 2.1Å</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=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | {{STRUCTURE_2ao5| PDB=2ao5 | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ao5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ao5 OCA], [https://pdbe.org/2ao5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ao5 RCSB], [https://www.ebi.ac.uk/pdbsum/2ao5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ao5 ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''Crystal structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G-U base pairs'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Balasundaresan D]] |
| - | The crystal structure of a self-complementary RNA duplex r(GGCG(Br)UGCGCU)(2) with terminal G.U and internal tandem G.U base pairs has been determined at 2.1 Angstroms resolution. The crystals belong to the tetragonal space group P4(3), with unit-cell parameters a = b = 37.69, c = 96.28 Angstroms and two duplexes in the asymmetric unit. The two strands of each duplex are related by a pseudodyad axis. The structure was refined to final R(work) and R(free) values of 20.9 and 25.3%, respectively. The duplexes stack in an end-to-end manner, forming infinite columns along the c axis. This is the first structural study of an RNA duplex containing G.U pairs at the termini. The stacking overlaps of the terminal G.U base pairs with their adjacent Watson-Crick base pairs are larger than those of Watson-Crick base pairs of the 5'-YR-3'/3'-RY-5' type. The terminal G.U base pairs of neighbouring duplexes are also stacked with each other. An alternating underwound-overwound pattern of the twist angles is seen at each step along the duplex. This observation is typical for internal tandem G.U pairs, while the terminal G.U base pairs exhibit high twist angles with the adjacent Watson-Crick pairs. The 3'-side of U of the internal G.U base pair, which is unstacked, appears to be stabilized by pi-cation interaction with an Mg(2+) ion.
| + | [[Category: Fukamizu A]] |
| - | | + | [[Category: Kumar PK]] |
| - | ==About this Structure== | + | [[Category: Mizuno H]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AO5 OCA].
| + | [[Category: Suto K]] |
| - | | + | [[Category: Utsunomiya R]] |
| - | ==Reference==
| + | |
| - | Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs., Utsunomiya R, Suto K, Balasundaresan D, Fukamizu A, Kumar PK, Mizuno H, Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):331-8. Epub 2006, Feb 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16510980 16510980]
| + | |
| - | [[Category: Balasundaresan, D.]] | + | |
| - | [[Category: Fukamizu, A.]] | + | |
| - | [[Category: Kumar, P K.]] | + | |
| - | [[Category: Mizuno, H.]] | + | |
| - | [[Category: Suto, K.]] | + | |
| - | [[Category: Utsunomiya, R.]] | + | |
| - | [[Category: G-u base pair]]
| + | |
| - | [[Category: Rna duplex]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 19:16:40 2008''
| + | |
