4DY8

Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb4DY8/pdb
• NAKB: 4DY8

• Classification: DNA
• Mutation(s): No 


• Deposited: 2012-02-28 Released: 2012-11-28 
• Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.262 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Literature

Interactions of Mn(2+) with a non-self-complementary Z-type DNA duplex

Mandal, P.K., Venkadesh, S., Gautham, N.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1420-1426

• PubMed: 23192018 
• DOI: https://doi.org/10.1107/S1744309112041759
• Primary Citation of Related Structures:  
  4DWY, 4DY8


• PubMed Abstract: 
  

  Crystal structures of the hexanucleotide d(CACGCG)·d(CGCGTG) were determined in two crystal lattices when different concentrations of the counterion Mn2+ were used in crystallization. The availability of Mn2+ during the crystallization process appears to play an important role in inducing different crystal packings that lead to crystals belonging to the two space groups P2(1) and P6(5). Analysis of the molecular interactions of Mn2+ with the Z-form duplexes shows direct coordination to the purine residues G and A.

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Organizational Affiliation: 

CAS in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India.

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 4.85 kDa 
• Atom Count: 357 
• Modelled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')	A	6	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')	B	6	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*G)-3')	C, D	2	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.262 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.213	α = 90
b = 35.213	β = 90
c = 44.452	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-28 
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Revision History  

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations