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| - | [[Image:420d.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES== |
| - | |PDB= 420d |SIZE=350|CAPTION= <scene name='initialview01'>420d</scene>, resolution 1.900Å
| + | <StructureSection load='420d' size='340' side='right'caption='[[420d]], [[Resolution|resolution]] 1.90Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[420d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=420D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=420D FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=420d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=420d OCA], [https://pdbe.org/420d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=420d RCSB], [https://www.ebi.ac.uk/pdbsum/420d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=420d ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=420d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=420d OCA], [http://www.ebi.ac.uk/pdbsum/420d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=420d RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES'''
| + | [[Category: Mitra SN]] |
| - | | + | [[Category: Pan B]] |
| - | | + | [[Category: Sundaralingam M]] |
| - | ==Overview==
| + | |
| - | G.A mispairs are one of the most common noncanonical structural motifs of RNA. The 1.9 A resolution crystal structure of the RNA 16-mer r(GCAGAGUUAAAUCUGC)2 has been determined with two isolated or nonadjacent G.A mispairs. The molecule crystallizes with one duplex in the asymmetric unit in space group R3 and unit cell dimensions a = b = c = 49.24 A and alpha = beta = gamma = 51.2 degrees. It is the longest known oligonucleotide duplex at this resolution and isomorphous to the 16-mer duplex with the C.A+ mispairs [Pan, et al., (1998) J. Mol. Biol. 283, 977-984]. The C.A+ mispair behaves like a wobble pair while the G.A+ does not. The G.A mispairs are protonated at N1 of the adenines as in the C.A+ mispairs, and two hydrogen bonds in the G(syn).A+(anti) conformation are formed. The syn guanine is stabilized by an intranucleotide hydrogen bond between the 2-amino and the 5'-phosphate groups. The G(syn).A+(anti) conformation can provide a different surface for recognition in the grooves compared to other G.A hydrogen bonding schemes. The major groove is widened between the two mispairs allowing access to ligands. One of the 3-fold axes is occupied by a sodium ion and a water molecule, while a second is occupied by another water molecule.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 420D is a [[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=420D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs., Pan B, Mitra SN, Sundaralingam M, Biochemistry. 1999 Mar 2;38(9):2826-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10052954 10052954]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Mitra, S N.]] | + | |
| - | [[Category: Pan, B.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: a-rna structure]]
| + | |
| - | [[Category: mismatch a rna]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:01 2008''
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