3EY1 image
Deposition Date 2008-10-17
Release Date 2009-04-28
Last Version Date 2023-09-06
Entry Detail
PDB ID:
3EY1
Keywords:
HYDROLASE/DNA
Title:
A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution
Biological Source:
Source Organism:
Bacillus halodurans (Taxon ID: 86665)
(Taxon ID: )
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.60 Å
R-Value Free:
0.26
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
3EY1 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribonuclease H
Gene (Uniprot):rnhA
Mutations:D132N
Chain IDs:A
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus halodurans
UniProt ID:Q9KEI9 EC:3.1.13.2
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'
Chain IDs:B
Chain Length:12
Number of Molecules:1
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
USM B DU ?
Ligand Molecules
GOL
Primary Citation
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
Chem.Commun.(Camb.) 15 2017 2019 (2009)
PMID: 19333476 DOI: 10.1039/b822781k

Abstact

Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
3EY2
3EY3