351D | pdb_0000351d

X-RAY CRYSTAL STRUCTURES OF THE HEXAMER DCACGCG: CRYSTALS GROWN IN THE PRESENCE OF RUTHENIUM (II) HEXAMMINE CHLORIDE

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 1997-08-30 Released: 1997-09-30 
  • Deposition Author(s): Karthe, P., Gautham, N.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of d(CACGCG).d(CGCGTG) in crystals grown in the presence of ruthenium III hexammine chloride.

Karthe, P., Gautham, N.

(1998) Acta Crystallogr D Biol Crystallogr 54: 501-509

  • DOI: https://doi.org/10.1107/s0907444997013954
  • Primary Citation of Related Structures:  
    351D

  • PubMed Abstract: 

    Hexammine ions are strong inducers of the transition from the B-form to the left-handed Z-form in DNA. Here the structure of d(CACGCG). d(CGCGTG) obtained from crystals grown from a drop containing [Ru(NH3)6]Cl3 is reported. The structure is clearly characterized as Z-DNA. When compared with the structure of d(CACGCG).d(CGCGTG)/MgCl2 and that of d(CGCGCG)2, subtle differences are seen, most noticeably in the water structure. Since stable well diffracting crystals grow easily in the presence of [Ru(NH3)6]Cl3 and since this ion is not visible in the electron density it is concluded that the ion plays a non-specific role in stabilizing Z-DNA.

    • Organizational Affiliation: 

    Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India. crystal@giasmd01.vsnl.net.in


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')6N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')6N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 17.88α = 90
b = 30.87β = 90
c = 44.83γ = 90
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-09-30
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references