3EY3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.147 

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:  

  • 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 doe ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'A,B,C,D12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
B, D
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
A, B, C, D
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
USM
Query on USM
A, B, C, D
DNA LINKINGC10 H15 N2 O8 P SDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.074α = 90.00
b = 43.218β = 90.00
c = 88.712γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
XDSdata reduction
XDSdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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