405d
From Proteopedia
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|PDB= 405d |SIZE=350|CAPTION= <scene name='initialview01'>405d</scene>, resolution 2.50Å | |PDB= 405d |SIZE=350|CAPTION= <scene name='initialview01'>405d</scene>, resolution 2.50Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |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=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=405d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=405d OCA], [http://www.ebi.ac.uk/pdbsum/405d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=405d RCSB]</span> | ||
}} | }} | ||
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[[Category: a-rna double helix]] | [[Category: a-rna double helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:36:50 2008'' |
Revision as of 02:36, 31 March 2008
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| , resolution 2.50Å | |||||||
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| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF A 16-MER RNA DUPLEX R(GCAGACUUAAAUCUGC)2 WITH WOBBLE LIKE A.C MISMATCHES
Overview
The crystal structure of a 16-mer, the longest known RNA duplex, has been determined at 2.5 A resolution. The hexadecamer r(GCAGACUUAAAUCUGC) contains isolated C.A/A.C mismatches with two hydrogen bonds. The two hydrogen bonds in the mismatches suggests that N1 of A is protonated even though the crystallization was done at neutral pH. Therefore, the C.A mismatch is a C.A+ wobble similar to the G.U wobble. The two C.A+ pairs are isolated by four Watson-Crick pairs and flanked by five Watson-Crick base-pairs on either sides. Kinks/bends of 20 degrees are observed at the wobble sites. The Watson-Crick base-pair A5.U26 on the 5'-side of the first C6.A27(+) wobble has a twist angle of 27 degrees compared to the 3'-side U7.A28 pair of 36 degrees. The twist angles are reversed (37 degrees and 26 degrees) in the second A11(+).C22 wobble because of the approximate dyad in the molecule, the flanking base-pair sequences are A.U pairs. The wobbles expand the major groove to 7.1 A/7.3 A. The duplexes form helical columns and are tightly packed around the 31-screw axis. The minor grooves of adjacent columns in juxtaposition interact through the O2' atoms and the anionic phosphate oxygen atoms.Copyright 1998 Academic Press.
About this Structure
405D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C.A+ mismatches., Pan B, Mitra SN, Sundaralingam M, J Mol Biol. 1998 Nov 13;283(5):977-84. PMID:9799637
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