417D

A THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.

Schuerman, G.S.Van Meervelt, L.Loakes, D.Brown, D.M.Kong Thoo Lin, P.Moore, M.H.Salisbury, S.A.

(1998) J.Mol.Biol. 282: 1005-1011

  • DOI: 10.1006/jmbi.1998.2080

  • PubMed Abstract: 
  • The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that ...

    The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inconsistent with other evidence from hybridisation and NMR studies of P-containing oligonucleotides, which suggests that, while P can form stable base-pairs with either A or G, thymine-like properties are more pronounced. Thermal denaturation experiments over a range of solution pH values indicate that protonation of the P.A base-pairs is unlikely to be responsible for the anomalous behaviour. No specific crystal packing effects can be identfied as an explanation, and it is concluded that base stacking and other interactions between nucleotide residues in Z-DNA are responsible.


    Organizational Affiliation

    Departement Scheikunde, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Heverlee, B-3001, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*CP*GP*(C46)P*G)-3')A,B6N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
C46
Query on C46
A, B
DNA LINKINGC11 H16 N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 17.338α = 90.00
b = 31.432β = 90.00
c = 44.486γ = 90.00
Software Package:
Software NamePurpose
SHELXL-93refinement
ROTAVATA)data scaling
DENZOdata reduction
AMoREphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-30
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance