3EIL

Structure of B-DNA d(CGTTAATTAACG)2 in the presence of Manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The interaction of manganese ions with DNA

Millonig, H.Pous, J.Gouyette, C.Subirana, J.A.Campos, J.L.

(2009) J.Inorg.Biochem. 103: 876-880

  • DOI: 10.1016/j.jinorgbio.2009.03.004

  • PubMed Abstract: 
  • We present the structure of the duplex formed by a fragment of auto-complementary DNA with the sequence d(CGTTAATTAACG). The structure was determined by X-ray crystallography. Up to date it is the first structure presenting the interaction between a ...

    We present the structure of the duplex formed by a fragment of auto-complementary DNA with the sequence d(CGTTAATTAACG). The structure was determined by X-ray crystallography. Up to date it is the first structure presenting the interaction between a DNA oligonucleotide and manganese ions. The presence of Mn2+ creates bonds among the N7 atom of guanines and phosphates. These bonds stabilize and determine the crystallographic network in a P3(2) space group, unusual in oligonucleotide crystals. The crystal structure observed is compared with those found in the presence of Mg2+, Ca2+ and Ni2+, which show different kinds of interactions. The double helices show end-to-end interactions, in a manner that the terminal guanines interact with the minor groove of the neighboring duplex, while the terminal cytosines are disordered. We have chosen this sequence since it contains a TTAA repeat. Such repeats are very rare in all genomes. We suggest that this sequence may be very susceptible to the formation of closely spaced thymine dimers.


    Organizational Affiliation

    Departament d'Enginyeria Quimica, ETSEIB-UPC, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*DCP*DGP*DTP*DTP*DAP*DAP*DTP*DTP*DAP*DAP*DCP*DG)-3'A,B,C,D,E,F12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.235 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 43.795α = 90.00
b = 43.795β = 90.00
c = 98.345γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance