Sodium in PDB 1xpe: Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site

The structure of Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site, PDB code: 1xpe was solved by E.Ennifar, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.73 / 1.94
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	27.426, 114.573, 95.448, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 25.5

The structure of Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site (pdb code 1xpe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site, PDB code: 1xpe:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:43.1 occ:1.00 O B:HOH322 2.6 42.2 1.0 N3 A:G12 2.8 29.5 1.0 N2 A:G12 3.3 27.8 1.0 C2 A:G12 3.4 29.7 1.0 O A:HOH248 3.7 28.8 0.8 C4 A:G12 3.8 29.4 1.0 C1' A:G12 3.8 31.1 1.0 N3 B:G14 4.0 27.5 1.0 N2 B:G14 4.0 29.0 1.0 O B:HOH208 4.0 47.7 1.0 O2' A:G12 4.0 32.3 1.0 N9 A:G12 4.2 31.2 1.0 C2' A:G12 4.3 33.2 1.0 C2 B:G14 4.3 28.0 1.0 N1 A:G12 4.7 28.8 1.0 O4' A:G12 4.9 32.6 1.0 O B:HOH227 4.9 50.1 1.0 O2' B:G14 5.0 30.4 1.0 O4' A:C13 5.0 33.5 1.0 C4 B:G14 5.0 27.7 1.0

Sodium binding site 2 out of 4 in the Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na111 b:42.9 occ:1.00 O2' A:C1 2.8 31.5 1.0 O2 A:C1 2.9 25.2 1.0 C2' A:C1 3.5 30.0 1.0 O4' A:U2 3.5 34.2 1.0 C1' A:C1 3.7 28.5 1.0 C2 A:C1 4.0 26.0 1.0 N2 A:G23 4.1 30.3 1.0 C1' A:U2 4.3 35.2 1.0 N1 A:C1 4.4 25.8 1.0 C4' A:U2 4.5 35.6 1.0 C5' A:U2 4.8 33.5 1.0 N1 A:U2 4.8 35.0 1.0 O4' A:C1 4.9 27.8 1.0 C6 A:U2 4.9 35.3 1.0 C3' A:C1 4.9 30.9 1.0

Sodium binding site 3 out of 4 in the Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:41.9 occ:0.83 O2 B:C13 2.7 29.1 1.0 O B:HOH201 2.8 32.9 0.5 O2' B:C13 3.5 34.2 1.0 C1' B:C13 3.7 30.7 1.0 N2 A:G12 3.7 27.8 1.0 C2 B:C13 3.8 30.5 1.0 C2' B:C13 3.9 32.7 1.0 N1 B:C13 4.3 30.0 1.0 O B:HOH259 4.3 47.6 1.0 N2 B:G12 4.3 22.6 1.0 O2 A:C13 4.4 31.0 1.0 O4' B:G14 4.5 31.2 1.0 O4' B:C13 4.8 29.7 1.0 N3 B:C13 4.9 30.4 1.0 C1' B:G14 5.0 30.1 1.0

Sodium binding site 4 out of 4 in the Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:37.7 occ:0.96 O B:HOH303 2.4 46.1 1.0 O2 B:C1 2.9 33.5 1.0 O2' B:C1 3.0 37.5 1.0 O4' B:U2 3.5 33.4 1.0 C2' B:C1 3.6 36.3 1.0 N2 B:G23 3.8 34.0 1.0 C1' B:C1 3.9 36.4 1.0 C2 B:C1 4.0 33.5 1.0 C1' B:U2 4.2 34.8 1.0 C4' B:U2 4.5 34.1 1.0 N1 B:C1 4.5 34.1 1.0 N1 B:U2 4.7 32.0 1.0 C5' B:U2 4.8 35.2 1.0 C6 B:U2 4.9 31.5 1.0

E.Ennifar, P.Dumas. Polymorphism of Bulged-Out Residues in Hiv-1 Rna Dis Kissing Complex and Structure Comparison with Solution Studies J.Mol.Biol. V. 356 771 2006.
ISSN: ISSN 0022-2836
PubMed: 16403527
DOI: 10.1016/J.JMB.2005.12.022