1idw
From Proteopedia
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|PDB= 1idw |SIZE=350|CAPTION= <scene name='initialview01'>1idw</scene>, resolution 1.8Å | |PDB= 1idw |SIZE=350|CAPTION= <scene name='initialview01'>1idw</scene>, resolution 1.8Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=RHD:RHODIUM+HEXAMINE+ION'>RHD</scene> | + | |LIGAND= <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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>, <scene name='pdbligand=UCL:5-CHLORO-2'-DEOXYURIDINE+5'-(DIHYDROGEN+PHOSPHATE)'>UCL</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1icg|1ICG]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1idw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1idw OCA], [http://www.ebi.ac.uk/pdbsum/1idw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1idw RCSB]</span> | ||
}} | }} | ||
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[[Category: Prange, T.]] | [[Category: Prange, T.]] | ||
[[Category: Saludjian, P.]] | [[Category: Saludjian, P.]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: RHD]] | ||
[[Category: c-u mismatch]] | [[Category: c-u mismatch]] | ||
[[Category: g-u mismatch]] | [[Category: g-u mismatch]] | ||
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[[Category: rna/dna hybrid]] | [[Category: rna/dna hybrid]] | ||
| - | ''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 21:18:25 2008'' |
Revision as of 18:18, 30 March 2008
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| , resolution 1.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Related: | 1ICG
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF RH(NH3)6+++
Overview
In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions.
About this Structure
1IDW is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues., Cruse W, Saludjian P, Neuman A, Prange T, Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1609-13. Epub 2001, Oct 25. PMID:11679725
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