4DY8

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

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


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

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*G)-3')
C, D
2N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download Ideal Coordinates CCD File 
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 = 35.213α = 90
b = 35.213β = 90
c = 44.452γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
AUTOMARdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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