2HTO | pdb_00002hto

Ruthenium hexammine ion interactions with Z-DNA

• PDB DOI: https://doi.org/10.2210/pdb2HTO/pdb
• NAKB: 2HTO

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-07-26 Released: 2006-08-08 
• Deposition Author(s): Bharanidharan, D., Thiyagarajan, S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Hexammineruthenium(III) ion interactions with Z-DNA

Bharanidharan, D., Thiyagarajan, S., Gautham, N.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 1008-1013

• PubMed: 18084080 
• DOI: https://doi.org/10.1107/S1744309107047781
• Primary Citation of Related Structures:  
  2HTO, 2HTT


• PubMed Abstract: 
  

  The hexamer duplex d(CGCGCA).d(TGCGCG) was crystallized with hexammineruthenium(III) ions in an orthorhombic space group; the crystals diffracted to 1.54 A resolution. Strong ion interactions with the adenine base induce a tautomeric shift from the amino to the imino form. Consequently, the A.T base pairing is disrupted. This structural study may be relevant to metal toxicity.

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Organizational Affiliation: 

Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.82 kDa 
• Atom Count: 307 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DA)-3')	A	6	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DTP*DGP*DCP*DGP*DCP*DG)-3')	B	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NRU	C [auth A]	RUTHENIUM (III) HEXAAMINE ION H18 N6 Ru HOOVQFBYNWLMGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.953	α = 90
b = 30.821	β = 90
c = 44.596	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Bharanidharan, D., Thiyagarajan, S., Gautham, N.

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description