1RDE

NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 11 
  • Conformers Submitted: 11 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+.

Mao, X.Marky, L.A.Gmeiner, W.H.

(2004) J.Biomol.Struct.Dyn. 22: 25-33

  • DOI: 10.1080/07391102.2004.10506977

  • PubMed Abstract: 
  • The structure of thrombin-binding DNA aptamer complexed with a single Sr2+ ion (Sr2+:TBA complex) has been determined using NMR spectroscopy and restrained molecular dynamics simulations. The quadruplex structure for the Sr2+:TBA complex is similar i ...

    The structure of thrombin-binding DNA aptamer complexed with a single Sr2+ ion (Sr2+:TBA complex) has been determined using NMR spectroscopy and restrained molecular dynamics simulations. The quadruplex structure for the Sr2+:TBA complex is similar in topology, but distinct in structure, from that previously reported for the K+:TBA complex. The inter-tetrad distance of the Sr2+:TBA complex is 3.8 angstroms, or 0.7 angstroms larger than in the K+:TBA complex. This substantial difference can be attributed to a different binding site for Sr2+ in the Sr2+:TBA complex than for K+ in the K+:TBA complex. The Sr2+:TBA complex assumes a 1:1 stoichiometry, and it is very likely that the Sr2+ ion simultaneously interacts with the eight O6 atoms of the two G-tetrads. The results indicate that quadruplex DNA structures are highly sensitive to the presence of specific metal ions. The binding of specific metal ions may modulate the biological activity of quadruplex DNA structures in vivo.


    Organizational Affiliation

    Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157-1016, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Thrombin-binding DNA aptamerA15N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 11 
  • Conformers Submitted: 11 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance