Sodium in PDB 1y6t: Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked

The structure of Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked, PDB code: 1y6t was solved by E.Ennifar, P.Walter, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.97 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.797, 58.797, 65.097, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.5

The structure of Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked also contains other interesting chemical elements:

Cobalt

(Co)

5 atoms

The binding sites of Sodium atom in the Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked (pdb code 1y6t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked, PDB code: 1y6t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Na120 b:38.3 occ:0.50 N2 B:G7 2.6 38.5 0.5 C2 B:G7 3.8 38.5 0.5 N2 B:G7 3.8 32.3 0.5 N2 B:G9 3.9 35.5 0.5 NA B:NA130 4.0 21.2 0.5 C1' A:A18 4.3 39.9 1.0 O4' A:A18 4.3 40.6 1.0 N2 B:G9 4.3 37.7 0.5 C2 B:G9 4.3 35.6 0.5 N3 B:G9 4.5 35.6 0.5 N3 B:G7 4.5 38.5 0.5 O2 A:C17 4.5 44.0 1.0 N1 B:G7 4.6 38.6 0.5 N3 B:G9 4.8 37.7 0.5 N9 A:A18 4.9 38.6 1.0 C2 B:G9 4.9 37.6 0.5 C2 B:G7 4.9 32.6 0.5

Sodium binding site 2 out of 2 in the Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Na130 b:21.2 occ:0.50 N3 B:G7 1.9 38.5 0.5 C2 B:G7 2.5 38.5 0.5 N2 B:G7 2.6 38.5 0.5 O2' B:G7 2.7 34.0 0.5 C4 B:G7 3.0 38.4 0.5 N3 B:G7 3.1 32.7 0.5 N3 B:G9 3.1 37.7 0.5 C4 B:G9 3.2 35.6 0.5 C4 B:G9 3.3 37.8 0.5 N9 B:G9 3.3 36.0 0.5 N3 B:G9 3.4 35.6 0.5 C2' B:G7 3.4 34.0 0.5 C1' B:G7 3.6 38.2 0.5 N9 B:G9 3.6 38.1 0.5 C1' B:G9 3.7 38.2 0.5 N9 B:G7 3.7 38.4 0.5 C2' B:G7 3.7 38.2 0.5 C5 B:G9 3.7 35.5 0.5 C1' B:G7 3.7 33.6 0.5 O2' B:G7 3.7 38.2 0.5 C1' B:G9 3.8 36.1 0.5 C2 B:G9 3.8 37.6 0.5 N2 B:G7 3.8 32.3 0.5 N1 B:G7 3.9 38.6 0.5 C2 B:G7 3.9 32.6 0.5 C8 B:G9 3.9 35.7 0.5 C2 B:G9 4.0 35.6 0.5 NA B:NA120 4.0 38.3 0.5 C4 B:G7 4.0 32.9 0.5 C5 B:G9 4.1 37.8 0.5 N7 B:G9 4.1 35.7 0.5 O4' B:G9 4.3 38.3 0.5 C5 B:G7 4.3 38.5 0.5 N9 B:G7 4.3 33.2 0.5 N2 B:G9 4.3 37.7 0.5 C6 B:G9 4.3 35.4 0.5 N1 B:G9 4.4 35.5 0.5 C8 B:G9 4.4 38.0 0.5 N1 B:G9 4.5 37.5 0.5 O4' B:G9 4.5 36.2 0.5 C6 B:G7 4.7 38.7 0.5 C6 B:G9 4.7 37.6 0.5 N7 B:G9 4.7 37.9 0.5 N2 B:G9 4.8 35.5 0.5 C3' B:G7 4.9 34.3 0.5 O4' B:G7 4.9 38.3 0.5 C2' B:G9 4.9 38.1 0.5 O4' B:G7 5.0 34.0 0.5 C8 B:G7 5.0 38.3 0.5

E.Ennifar, P.Walter, P.Dumas. A Crystallographic Study of the Binding of 13 Metal Ions to Two Related Rna Duplexes Nucleic Acids Res. V. 31 2671 2003.
ISSN: ISSN 0305-1048
PubMed: 12736317
DOI: 10.1093/NAR/GKG350