Sodium in PDB 2dyw: A Backbone Binding Dna Complex

The structure of A Backbone Binding Dna Complex, PDB code: 2dyw was solved by S.Komeda, T.Moulaei, K.K.Woods, M.Chikuma, N.P.Farrell, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	5.50 / 1.13
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	23.675, 41.692, 65.651, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / 23.2

The structure of A Backbone Binding Dna Complex also contains other interesting chemical elements:

Platinum

(Pt)

4 atoms

The binding sites of Sodium atom in the A Backbone Binding Dna Complex (pdb code 2dyw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the A Backbone Binding Dna Complex, PDB code: 2dyw:

Sodium binding site 1 out of 1 in the A Backbone Binding Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Backbone Binding Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:16.1 occ:1.00 O B:HOH3004 2.3 19.0 1.0 O6 B:DG10 2.4 12.3 1.0 O A:HOH3001 2.4 19.6 1.0 O A:HOH3002 2.5 21.0 1.0 O A:HOH3005 2.5 35.7 1.0 O B:HOH3003 2.6 23.9 1.0 C6 B:DG10 3.4 11.9 1.0 O A:HOH2108 3.6 41.5 1.0 O6 A:DG2 4.0 11.4 1.0 N7 B:DG10 4.0 12.9 1.0 N4 A:DC3 4.0 11.8 1.0 C5 B:DG10 4.1 12.1 1.0 N4 B:DC9 4.1 13.3 1.0 O A:HOH2012 4.2 25.6 1.0 O B:HOH2064 4.3 28.6 1.0 C5 B:DC9 4.5 12.4 1.0 C4 B:DC9 4.6 13.8 1.0 O A:HOH2020 4.6 25.6 1.0 N7 A:DG2 4.6 11.7 1.0 N1 B:DG10 4.7 10.8 1.0 O A:HOH2095 4.7 46.1 1.0 C6 A:DG2 4.8 9.2 1.0 O A:HOH2056 4.9 37.4 1.0

S.Komeda, T.Moulaei, K.K.Woods, M.Chikuma, N.P.Farrell, L.D.Williams. A Third Mode of Dna Binding: Phosphate Clamps By A Polynuclear Platinum Complex J.Am.Chem.Soc. V. 128 16092 2006.
ISSN: ISSN 0002-7863
PubMed: 17165762
DOI: 10.1021/JA062851Y