115D

ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

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This is version 1.2 of the entry. See complete history

Literature

Ordered water structure in an A-DNA octamer at 1.7 A resolution.

Kennard, O.Cruse, W.B.Nachman, J.Prange, T.Shakked, Z.Rabinovich, D.

(1986) J.Biomol.Struct.Dyn. 3: 623-647

  • DOI: 10.1080/07391102.1986.10508452

  • PubMed Abstract: 
  • The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was refined to a resolution of 1.7 A using combined diffractometer and synchrotron data. The analysis was carried out independently in two laboratories using different procedures. Alth ...

    The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was refined to a resolution of 1.7 A using combined diffractometer and synchrotron data. The analysis was carried out independently in two laboratories using different procedures. Although the final results are identical the comparison of the two approaches highlights potential problems in the refinement of oligonucleotides when only limited data are available. As part of the analysis the positions of 84 solvent molecules in the asymmetric unit were established. The DNA molecule is highly solvated, particularly the phosphate-sugar back-bone and the functional groups of the bases. The major groove contains, in the central BrU-A-BrU-A region, a ribbon of water molecules forming closed pentagons with shared edges. These water molecules are linked to the base O and N atoms and to the solvent chains connecting the O-1 phosphate oxygen atoms on each strand. The minor groove is also extensively hydrated with a continuous network in the central region and other networks at each end. The pattern of hydration is briefly compared with that observed in the structure of a B-dodecamer.


    Related Citations: 
    • Crystalline A-DNA. The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C)
      Shakked, Z.,Rabinovich, D.,Cruse, W.B.T.,Egert, E.,Kennard, O.,Sala, G.,Salisbury, S.A.,Viswamitra, M.A.
      (1981) Proc.R.Soc.London,Ser.B 213: 479
    • Sequence-Dependent Conformation of an A-DNA Double Helix. The Crystal Structure of the Octamer d(G-G-T-A-T-A-C-C)
      Shakked, Z.,Rabinovich, D.,Kennard, O.,Cruse, W.B.T.,Salisbury, S.A.,Viswamitra, M.A.
      (1983) J.Mol.Biol. 166: 183
    • Coexistence of A-and B-Form DNA in a Single Crystal Lattice
      Doucet, J.,Benoit, J.-P.,Cruse, W.B.T.,Prange, T.,Kennard, O.
      (1989) Nature 337: 190


    Organizational Affiliation

    University Chemical Laboratory, Cambridge, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*(BRU)P*AP*(BRU)P*AP*CP*C)-3')A,B8N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
A, B
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 45.084α = 90.00
b = 45.084β = 90.00
c = 41.720γ = 120.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance