Sodium in PDB 1zf9: Ggg Duplex A-Dna

The structure of Ggg Duplex A-Dna, PDB code: 1zf9 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)	18.99 / 1.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	23.280, 45.310, 47.550, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 25.9

The binding sites of Sodium atom in the Ggg Duplex A-Dna (pdb code 1zf9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ggg Duplex A-Dna, PDB code: 1zf9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ggg 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 Ggg Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na64 b:10.7 occ:1.00 O A:HOH88 2.6 12.1 1.0 C1' A:DC1 2.6 10.5 1.0 O A:HOH79 2.9 12.2 1.0 C2' A:DC1 3.0 11.4 1.0 O4' A:DC1 3.0 11.8 1.0 C3' A:DC1 3.2 11.8 1.0 O3' A:DC1 3.3 11.2 1.0 C4' A:DC1 3.4 12.3 1.0 O A:HOH23 3.9 3.1 1.0 N1 A:DC1 4.0 10.0 1.0 O2 A:DC1 4.6 8.4 1.0 C2 A:DC1 4.8 9.6 1.0 C6 A:DC1 4.9 10.4 1.0 P A:DC2 4.9 9.2 1.0 C5' A:DC1 4.9 13.0 1.0

Sodium binding site 2 out of 2 in the Ggg Duplex A-Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ggg Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na35 b:9.5 occ:1.00 O B:HOH73 2.3 14.3 1.0 O B:HOH37 2.3 13.0 1.0 O B:HOH81 2.5 21.5 1.0 O6 B:DG17 2.5 1.8 1.0 O B:HOH47 2.5 14.5 1.0 N7 B:DG17 3.3 2.7 1.0 C6 B:DG17 3.3 2.0 1.0 C5 B:DG17 3.7 2.3 1.0 O6 B:DG16 4.2 1.1 1.0 N4 A:DC4 4.3 2.7 1.0 C8 B:DG17 4.6 3.1 1.0 N7 B:DG16 4.6 1.6 1.0 O6 B:DG18 4.6 2.1 1.0 N1 B:DG17 4.7 1.4 1.0 C6 B:DG16 4.8 1.5 1.0 N7 B:DG18 4.9 2.7 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