165d
From Proteopedia
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|PDB= 165d |SIZE=350|CAPTION= <scene name='initialview01'>165d</scene>, resolution 1.550Å | |PDB= 165d |SIZE=350|CAPTION= <scene name='initialview01'>165d</scene>, resolution 1.550Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=RHD:RHODIUM HEXAMINE ION'>RHD</scene> | + | |LIGAND= <scene name='pdbligand=BRU:5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=RHD:RHODIUM+HEXAMINE+ION'>RHD</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=165d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=165d OCA], [http://www.ebi.ac.uk/pdbsum/165d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=165d RCSB]</span> | ||
}} | }} | ||
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[[Category: Saludjian, P.]] | [[Category: Saludjian, P.]] | ||
[[Category: Strazewski, P.]] | [[Category: Strazewski, P.]] | ||
| - | [[Category: RHD]] | ||
[[Category: a-dna/rna]] | [[Category: a-dna/rna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
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[[Category: overhanging base]] | [[Category: overhanging base]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:28:48 2008'' |
Revision as of 15:28, 30 March 2008
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| , resolution 1.550Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE
Overview
The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two G.U and two C.U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G.U pair is a wobble base pair analogous to the G.T pair found in DNA fragments. The C.U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. The BrU.BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.
About this Structure
165D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure., Cruse WB, Saludjian P, Biala E, Strazewski P, Prange T, Kennard O, Proc Natl Acad Sci U S A. 1994 May 10;91(10):4160-4. PMID:7514296
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