Sodium in PDB 2oj0: Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked

The structure of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked, PDB code: 2oj0 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 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.538, 47.834, 58.681, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23

The structure of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked also contains other interesting chemical elements:

Potassium	(K)	5 atoms
Manganese	(Mn)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked (pdb code 2oj0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked, PDB code: 2oj0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Na262 b:40.3 occ:0.80 O A:HOH391 3.7 25.8 1.0 O4' B:G10 4.8 21.4 1.0 O2' A:C17 4.8 22.9 1.0 O4' A:C17 4.9 21.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Na315 b:40.8 occ:0.90 OP1 A:C13 2.5 12.7 1.0 P A:C13 3.6 10.8 1.0 O3' A:G12 3.6 12.3 1.0 C5' A:C13 4.0 12.5 1.0 O5' A:C13 4.2 9.1 1.0 OP2 A:C13 4.9 10.2 1.0 C3' A:G12 5.0 13.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Na209 b:18.1 occ:1.00 O B:HOH219 2.7 14.8 1.0 N4 B:C11 3.1 18.4 1.0 O B:HOH260 3.2 43.5 1.0 O B:HOH240 3.3 17.6 1.0 O B:HOH245 3.5 22.2 1.0 O B:HOH263 3.6 37.4 1.0 O A:HOH320 4.2 18.8 1.0 C4 B:C11 4.2 17.6 1.0 C5 B:C11 4.4 16.8 1.0 O6 B:G12 4.4 15.2 1.0 OP1 B:A9 4.4 26.9 1.0 O6 A:G14 4.6 10.6 1.0 O6 B:G10 4.7 20.9 1.0 MN B:MN204 4.8 27.2 1.0

E.Ennifar, P.Walter, P.Dumas. Cation-Dependent Cleavage of the Duplex Form of the Subtype-B Hiv-1 Rna Dimerization Initiation Site. Nucleic Acids Res. V. 38 5807 2010.
ISSN: ISSN 0305-1048
PubMed: 20460458
DOI: 10.1093/NAR/GKQ344