1N1O

Crystal Structure of a B-form DNA Duplex Containing (L)-alpha-threofuranosyl (3'-2') Nucleosides: A Four-Carbon Sugar is Easily Accommodated into the Backbone of DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of a B-Form DNA Duplex Containing (L)-alpha-Threofuranosyl (3'-->2') Nucleosides: A Four-Carbon Sugar Is Easily Accommodated into the Backbone of DNA

Wilds, C.J.Wawrzak, Z.Krishnamurthy, R.Eschenmoser, A.Egli, M.

(2002) J.Am.Chem.Soc. 124: 13716-13721


  • PubMed Abstract: 
  • (L)-alpha-Threofuranosyl-(3'-->2')-oligonucleotides (TNA) containing vicinally connected phosphodiester linkages undergo informational base pairing in an antiparallel strand orientation and are capable of cross-pairing with RNA and DNA. TNA is derive ...

    (L)-alpha-Threofuranosyl-(3'-->2')-oligonucleotides (TNA) containing vicinally connected phosphodiester linkages undergo informational base pairing in an antiparallel strand orientation and are capable of cross-pairing with RNA and DNA. TNA is derived from a sugar containing only four carbon atoms and is one of the simplest potentially natural nucleic acid alternatives investigated thus far in the context of a chemical etiology of nucleic acid structure. Compared to DNA and RNA that contain six covalent bonds per repeating nucleotide unit, TNA contains only five. We have determined the atomic-resolution crystal structure of the B-form DNA duplex [d(CGCGAA)Td(TCGCG)](2) containing a single (L)-alpha-threofuranosyl thymine (T) per strand. In the modified duplex base stacking interactions are practically unchanged relative to the reference DNA structure. The orientations of the backbone at the TNA incorporation sites are slightly altered in order to accommodate fewer atoms and covalent bonds. The conformation of the threose is C4'-exo with the 2'- and 3'-substituents assuming quasi-diaxial orientation.


    Organizational Affiliation

    Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*CP*GP*AP*AP*(TFT)P*TP*CP*GP*CP*G)-3'A,B12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TFT
Query on TFT
A, B
DNA LINKINGC9 H13 N2 O8 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.277α = 90.00
b = 40.080β = 90.00
c = 65.860γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SHELXL-97refinement
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-15
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description