1PLY

SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)


Experimental Data Snapshot

  • Method: FIBER DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Work: 0.230 

wwPDB Validation

Currently 1PLY does not have a wwPDB validation report.


This is version 1.2 of the entry. See complete history

Literature

Sodium ions and water molecules in the structure of poly(dA).poly(dT).

Chandrasekaran, R.Radha, A.Park, H.S.

(1995) Acta Crystallogr.,Sect.D 51: 1025-1035

  • DOI: 10.1107/S0907444995001880

  • PubMed Abstract: 
  • Analysis of X-ray diffraction data from a polycrystalline and well oriented fiber of the sodium salt of poly(dA).poly(dT) shows that this B'-DNA corresponds to a right-handed antiparallel tenfold double-helix of pitch 32.4 A, with C2'-endo furanose r ...

    Analysis of X-ray diffraction data from a polycrystalline and well oriented fiber of the sodium salt of poly(dA).poly(dT) shows that this B'-DNA corresponds to a right-handed antiparallel tenfold double-helix of pitch 32.4 A, with C2'-endo furanose rings in both strands. The helix contrasts itself from B-DNA in terms of a very narrow minor groove. Difference electron-density maps have revealed that a continuous spine of water molecules, two per base pair, propagates along this groove with the same symmetry as the DNA and establishes new links between the two strands. In addition to this hydrated DNA helix, the monoclinic unit cell (space group P2(1)) accommodates about 20 sodium ions and 12 water molecules in the vicinity of phosphate groups. These structured guest molecules provide an intricate network of bridges, ranging in size from a single sodium ion to a multiple sodium-water-water-sodium unit, connecting phosphate groups belonging to adjacent DNA helices. The crystallographic R value for this structure is 0.23 for a total of 102 reflections extending out to 3.2 A resolution.


    Organizational Affiliation

    Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*AP*AP*AP*A)-3')A5N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*TP*TP*T)-3')B5N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: FIBER DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Work: 0.230 
Software Package:
Software NamePurpose
LALSrefinement

Structure Validation

Currently 1PLY does not have a wwPDB validation report.



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-06-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance