3EY2

A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2008-10-17 Released: 2009-04-28 
  • Deposition Author(s): Egli, M., Pallan, P.S.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.125 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.

Pallan, P.S.Prakash, T.P.Li, F.Eoff, R.L.Manoharan, M.Egli, M.

(2009) Chem Commun (Camb) 15: 2017-2019

  • DOI: 10.1039/b822781k
  • Primary Citation of Related Structures:  
    3EY1, 3EY2, 3EY3

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3'A, B 10N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N3D
Query on N3D

Download Ideal Coordinates CCD File 
C [auth B]N-methylpropane-1,3-diamine
C4 H12 N2
QHJABUZHRJTCAR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.69α = 90
b = 42.92β = 90
c = 46.12γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2008-10-17 
  • Released Date: 2009-04-28 
  • Deposition Author(s): Egli, M., Pallan, P.S.

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description