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 1.3 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: https://doi.org/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.

    • 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
MoleculeChains LengthOrganismImage
5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3'
A, B
10N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
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

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View more in-depth experimental data
Entry History 

Deposition Data

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
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description