Sodium in PDB 1y3o: Hiv-1 Dis Rna Subtype F- Mn Soaked

The structure of Hiv-1 Dis Rna Subtype F- Mn Soaked, PDB code: 1y3o 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)	10.00 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	27.341, 117.358, 94.672, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 28

The structure of Hiv-1 Dis Rna Subtype F- Mn Soaked also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Manganese	(Mn)	4 atoms

The binding sites of Sodium atom in the Hiv-1 Dis Rna Subtype F- Mn Soaked (pdb code 1y3o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hiv-1 Dis Rna Subtype F- Mn Soaked, PDB code: 1y3o:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Hiv-1 Dis Rna Subtype F- Mn 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 Rna Subtype F- Mn Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:62.2 occ:0.71 N6 B:A18 3.9 48.5 1.0 N4 B:C17 4.0 58.3 1.0 O4 B:U6 4.3 50.4 1.0 N4 B:C5 4.3 50.5 1.0

Sodium binding site 2 out of 3 in the Hiv-1 Dis Rna Subtype F- Mn 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 Rna Subtype F- Mn Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:57.4 occ:0.92 N4 A:C1 4.1 41.4 1.0 C5 A:C1 4.5 43.1 1.0 C4 A:C1 4.8 43.1 1.0

Sodium binding site 3 out of 3 in the Hiv-1 Dis Rna Subtype F- Mn Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hiv-1 Dis Rna Subtype F- Mn Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:40.3 occ:0.87 N7 B:G7 3.6 51.0 1.0 O4 B:U6 3.8 50.4 1.0 O6 B:G7 3.8 49.9 1.0 C5 B:U6 4.1 51.4 1.0 C4 B:U6 4.2 51.2 1.0 C5 B:G7 4.4 50.0 1.0 C6 B:G7 4.5 50.7 1.0 C8 B:G7 4.7 54.6 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