1JES

Crystal Structure of a Copper-Mediated Base Pair in DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Copper-Mediated Base Pair in DNA

Atwell, S.Meggers, E.Spraggon, G.Schultz, P.G.

(2001) J.Am.Chem.Soc. 123: 12364-12367


  • PubMed Abstract: 
  • Stable and selective DNA base pairing by metal coordination was recently demonstrated with nucleotides containing complementary pyridine-2,6-dicarboxylate (Dipic) and pyridine (Py) bases (Meggers, E.; Holland, P. L.; Tolman; W. B.; Romesberg, F. E.; ...

    Stable and selective DNA base pairing by metal coordination was recently demonstrated with nucleotides containing complementary pyridine-2,6-dicarboxylate (Dipic) and pyridine (Py) bases (Meggers, E.; Holland, P. L.; Tolman; W. B.; Romesberg, F. E.; Schultz, P. G. J. Am. Chem. Soc. 2000, 122, 10714-10715). To understand the structural consequences of introducing this novel base pair into DNA we have solved the crystal structure of a duplex containing the metallo-base pair. The structure shows that the bases pair as designed, but in a Z-DNA conformation. The structure also provides a structural explanation for the B- to Z-DNA transition in this duplex. Further solution studies demonstrate that the metallo-base pair is compatible with Z- or B-DNA conformations, depending on the duplex sequence.


    Related Citations: 
    • Structure of a B-DNA dodecamer: conformation and dynamics
      Drew, H.R.,Wing, R.M.,Takano, T.,Broka, C.,Tanaka, S.,Itakura, K.,Dickerson, R.E.
      (1981) Proc.Natl.Acad.Sci.USA 78: 2179
    • A Novel Copper-Mediated DNA Base Pair
      Meggers, E.,Holland, P.L.,Tolman, W.B.,Romesberg, F.E.,Schultz, P.G.
      (2000) J.Am.Chem.Soc. 122: 10714
    • Left-handed double helical DNA: variations in the backbone conformation
      Wang, A.G.-J.,Quigley, G.J.,Kolpak, F.J.,van Der Marel, G.,van Boom, J.H.,Rich, A.
      (1981) Science 211: 171


    Organizational Affiliation

    Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DRP
Query on DRP
A, B
DNA LINKINGC10 H14 N O6 P

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DPY
Query on DPY
A, B
DNA LINKINGC12 H14 N O10 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 25.343α = 90.00
b = 34.359β = 101.13
c = 31.093γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance