1XAM | pdb_00001xam

Cobalt hexammine induced tautameric shift in Z-DNA: structure of d(CGCGCA).d(TGCGCG) in two crystal forms.

• PDB DOI: https://doi.org/10.2210/pdb1XAM/pdb
• NAKB: 1XAM

• Classification: DNA
• Mutation(s): No 


• Deposited: 2004-08-26 Released: 2004-11-16 
• Deposition Author(s): Thiyagarajan, S., Rajan, S.S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.346 (Depositor), 0.368 (DCC) 
• R-Value Work: 
  0.273 (Depositor) 
• R-Value Observed: 
  0.279 (Depositor) 

Starting Model: experimental

Literature

Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms.

Thiyagarajan, S., Rajan, S.S., Gautham, N.

(2004) Nucleic Acids Res 32: 5945-5953

• PubMed: 15534365 
• DOI: https://doi.org/10.1093/nar/gkh919
• Primary Citation Related Structures: 
  1XA2, 1XAM


• PubMed Abstract: 
  

  We report here the crystal structure of the DNA hexamer duplex d(CGCGCA)*d(TGCGCG) at 1.71 A resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The interaction of this ion with the DNA helix results in a change of the adenine base from the common amino tautomeric form to the imino tautomer. Consequently the A:T base pair is disrupted from the normal Watson-Crick base pairing to a 'wobble' like base pairing. This change is accommodated easily within the helix, and the helical parameters are those expected for Z-DNA. When the cobalt hexammine concentration is decreased slightly in the crystallization conditions, the duplex crystallizes in a different, hexagonal space group, with two hexamer duplexes in the asymmetric unit. One of these is situated on a crystallographic 6-fold screw axis, leading to disorder. The tautomeric shift is not observed in this space group. We show that the change in inter-helix interactions that lead to the two different space groups probably arise from the small decrease in ion concentration, and consequently disordered positions for the ion.

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Organizational Affiliation: 
• Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.96 kDa 
• Atom Count: 349 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
CGCGCA	A	6	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
TGCGCG	B	6	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
TG	C [auth D], D [auth E]	2	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	E	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.346 (Depositor), 0.368 (DCC) 
• R-Value Work:  0.273 (Depositor) 
• R-Value Observed: 0.279 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.588	α = 90
b = 35.588	β = 90
c = 44.518	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
AUTOMAR	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-16 
Deposition Author(s): Thiyagarajan, S., Rajan, S.S., Gautham, N.

Revision History  

• Version 1.0: 2004-11-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description