420d: Difference between revisions
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[[Image:420d.gif|left|200px]] | [[Image:420d.gif|left|200px]] | ||
'''CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES''' | {{Structure | ||
|PDB= 420d |SIZE=350|CAPTION= <scene name='initialview01'>420d</scene>, resolution 1.900Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
420D is a [ | 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]. | ||
==Reference== | ==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:// | 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] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Mitra, S N.]] | [[Category: Mitra, S N.]] | ||
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[[Category: mismatch a rna]] | [[Category: mismatch a rna]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:08:04 2008'' | ||
Revision as of 17:08, 20 March 2008
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| 420d, resolution 1.900Å | |||||||||||||
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| Ligands: | NA | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES
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.
About this Structure
420D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
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:10052954
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