439d
From Proteopedia
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|PDB= 439d |SIZE=350|CAPTION= <scene name='initialview01'>439d</scene>, resolution 1.6Å | |PDB= 439d |SIZE=350|CAPTION= <scene name='initialview01'>439d</scene>, resolution 1.6Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=BA:BARIUM ION'>BA</scene> | + | |LIGAND= <scene name='pdbligand=BA:BARIUM+ION'>BA</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=439d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=439d OCA], [http://www.ebi.ac.uk/pdbsum/439d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=439d RCSB]</span> | ||
}} | }} | ||
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[[Category: Perbandt, M.]] | [[Category: Perbandt, M.]] | ||
[[Category: Vallazza, M.]] | [[Category: Vallazza, M.]] | ||
| - | [[Category: BA]] | ||
[[Category: a-rna]] | [[Category: a-rna]] | ||
[[Category: fragment of 5s rrna]] | [[Category: fragment of 5s rrna]] | ||
| - | ''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 05:37:13 2008'' |
Revision as of 02:37, 31 March 2008
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| , resolution 1.6Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'
Overview
The structure of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) has been determined at 1.6 A resolution and refined to a final R factor of 18.3% (R(free) = 24.1%). The sequence of the RNA fragment resembles domain E of Thermus flavus 5S rRNA. A previously undescribed wobble-like G.C base-pair formation is found. Owing to the observed hydrogen-bond network, it is proposed that the cytosine is protonated at position N3. The unusual base-pair formation is presumably strained by intermolecular interactions. In this context, crystal packing and particular intermolecular contacts may have direct influence on the three-dimensional structure. Furthermore, this structure includes two G.U wobble base pairs in tandem conformation, with the purines forming a so-called 'cross-strand G stack'.
About this Structure
439D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution., Perbandt M, Vallazza M, Lippmann C, Betzel C, Erdmann VA, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):219-24. PMID:11173467
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