2H0N

Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC.

Robeyns, K.Herdewijn, P.Van Meervelt, L.

(2008) J.Am.Chem.Soc. 130: 1979-1984

  • DOI: 10.1021/ja077313f
  • Also Cited By: 3LLN

  • PubMed Abstract: 
  • CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal str ...

    CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.


    Organizational Affiliation

    Katholieke Universiteit Leuven, Department of Chemistry, Biomolecular Architecture and BioMacS, Celestijnenlaan 200F, B-3001 Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'A,B8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2HP
Query on 2HP

Download SDF File 
Download CCD File 
A, B
DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
XTL
Query on XTL
A, B
DNA LINKINGC12 H17 N2 O7 PDT
XGL
Query on XGL
A, B
DNA LINKINGC12 H16 N5 O6 PDG
XAL
Query on XAL
A, B
DNA LINKINGC12 H16 N5 O5 PDA
XCL
Query on XCL
A, B
DNA LINKINGC11 H16 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Work: 0.158 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 41.455α = 90.00
b = 41.455β = 90.00
c = 65.580γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SHELXL-97refinement
SCALEPACKdata scaling
MAR345data collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-03-17
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Data collection, Refinement description