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420d
From Proteopedia
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|PDB= 420d |SIZE=350|CAPTION= <scene name='initialview01'>420d</scene>, resolution 1.900Å | |PDB= 420d |SIZE=350|CAPTION= <scene name='initialview01'>420d</scene>, resolution 1.900Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene> | + | |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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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> | ||
}} | }} | ||
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[[Category: Pan, B.]] | [[Category: Pan, B.]] | ||
[[Category: Sundaralingam, M.]] | [[Category: Sundaralingam, M.]] | ||
| - | [[Category: NA]] | ||
[[Category: a-rna structure]] | [[Category: a-rna structure]] | ||
[[Category: mismatch a rna]] | [[Category: mismatch a rna]] | ||
| - | ''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 05:37:01 2008'' |
Revision as of 02:37, 31 March 2008
| |||||||
| , resolution 1.900Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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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