Sodium in PDB 1zfa: Gga Duplex A-Dna

The structure of Gga Duplex A-Dna, PDB code: 1zfa 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)	19.23 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	23.930, 44.620, 46.780, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 30

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

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Gga Duplex A-Dna (pdb code 1zfa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Gga Duplex A-Dna, PDB code: 1zfa:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Gga 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 Gga Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na21 b:3.0 occ:1.00 O A:HOH83 2.1 12.6 1.0 O A:HOH34 2.2 9.0 1.0 O A:HOH116 3.0 13.9 1.0 O A:HOH37 4.2 9.9 1.0 OP2 A:DG10 4.3 3.9 1.0 N7 A:DG9 4.3 4.2 1.0 O A:HOH132 4.4 19.8 1.0 OP2 A:DG9 4.5 9.2 1.0 C8 A:DG9 4.7 3.0 1.0 N7 A:DG10 4.7 3.3 1.0 C5 A:DG9 4.9 4.1 1.0

Sodium binding site 2 out of 3 in the Gga 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 Gga Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na23 b:1.0 occ:1.00 O B:HOH73 2.3 5.0 1.0 O B:HOH141 2.9 16.9 1.0 O B:HOH68 3.0 12.1 1.0 OP1 B:DG20 4.4 2.5 1.0

Sodium binding site 3 out of 3 in the Gga Duplex A-Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gga Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na24 b:4.2 occ:1.00 O B:HOH142 2.3 7.7 1.0 O B:HOH36 2.4 14.5 1.0 O B:HOH82 2.7 4.2 1.0 O B:HOH144 3.1 14.9 1.0 O B:HOH156 3.3 16.2 1.0 O B:HOH78 3.5 10.6 1.0 N7 B:DG19 4.3 1.3 1.0 N7 B:DG20 4.5 1.9 1.0 O6 B:DG19 4.6 1.0 1.0 O6 B:DG20 4.7 1.0 1.0 O B:HOH86 4.7 4.9 1.0 O B:HOH129 4.8 14.5 1.0 O B:HOH96 4.9 14.1 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