1PLY

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

Summary for 1PLY

• Entry DOI: 10.2210/pdb1ply/pdb
• Descriptor: DNA (5'-D(P*AP*AP*AP*AP*A)-3'), DNA (5'-D(P*TP*TP*TP*TP*T)-3'), SODIUM ION, ... (4 entities in total)
• Functional Keywords: dna
• Total number of polymer chains: 2
• Total formula weight: 3226.98

Authors

Chandrasekaran, R.,Radha, A.,Park, H.-S. (deposition date: 1995-02-28, release date: 1995-06-03, Last modification date: 2024-02-14)

Primary citation

Chandrasekaran, R.,Radha, A.,Park, H.S.
Sodium ions and water molecules in the structure of poly(dA).poly(dT).
Acta Crystallogr.,Sect.D, 51:1025-1035, 1995

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 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.

PubMed: 15299771
DOI: 10.1107/S0907444995001880

Experimental method

FIBER DIFFRACTION (3.2 Å)