Sodium in PDB 1zf6: Tgg Duplex A-Dna

The structure of Tgg Duplex A-Dna, PDB code: 1zf6 was solved by F.A.Hays, A.T.Teegarden, Z.J.R.Jones, M.Harms, D.Raup, J.Watson, E.Cavaliere, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.95 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.239, 41.179, 44.410, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 30.6

The structure of Tgg Duplex A-Dna also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Tgg Duplex A-Dna (pdb code 1zf6). 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 Tgg Duplex A-Dna, PDB code: 1zf6:

Sodium binding site 1 out of 1 in the Tgg Duplex A-Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tgg Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na23 b:2.0 occ:1.00 O B:HOH34 2.5 8.0 1.0 O B:HOH79 2.6 7.5 1.0 O6 B:DG18 2.6 2.6 1.0 O B:HOH77 2.8 2.0 1.0 O B:HOH92 2.8 5.2 1.0 O B:HOH133 2.9 26.0 1.0 C6 B:DG18 3.5 2.3 1.0 N7 B:DG18 3.6 2.8 1.0 C5 B:DG18 3.9 2.0 1.0 N4 A:DC3 4.2 2.0 1.0 O6 B:DG19 4.3 2.0 1.0 N7 B:DG17 4.5 2.0 1.0 O6 B:DG17 4.5 3.1 1.0 O B:HOH103 4.5 5.2 1.0 O A:HOH31 4.6 3.5 1.0 N1 B:DG18 4.8 2.0 1.0 N4 A:DC2 4.8 4.5 1.0 C8 B:DG18 4.8 2.1 1.0 O B:HOH83 4.9 7.3 1.0

F.A.Hays, A.Teegarden, Z.J.Jones, M.Harms, D.Raup, J.Watson, E.Cavaliere, P.S.Ho. How Sequence Defines Structure: A Crystallographic Map of Dna Structure and Conformation. Proc.Natl.Acad.Sci.Usa V. 102 7157 2005.
ISSN: ISSN 0027-8424
PubMed: 15870206
DOI: 10.1073/PNAS.0409455102