Sodium in PDB 1xpf: Hiv-1 Subtype A Genomic Rna Dimerization Initiation Site

The structure of Hiv-1 Subtype A Genomic Rna Dimerization Initiation Site, PDB code: 1xpf 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)	19.63 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	28.364, 120.209, 97.969, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 24.6

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

Magnesium

(Mg)

3 atoms

The binding sites of Sodium atom in the Hiv-1 Subtype A Genomic Rna Dimerization Initiation Site (pdb code 1xpf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hiv-1 Subtype A Genomic Rna Dimerization Initiation Site, PDB code: 1xpf:

Sodium binding site 1 out of 1 in the Hiv-1 Subtype A 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 A Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:46.0 occ:1.00 O2 A:C1 2.8 23.6 1.0 O2' A:C1 2.9 27.4 1.0 C2' A:C1 3.5 27.4 1.0 O4' A:U2 3.6 29.7 1.0 C1' A:C1 3.8 26.4 1.0 C2 A:C1 3.9 23.5 1.0 N2 A:G23 4.1 26.6 1.0 C1' A:U2 4.4 30.1 1.0 N1 A:C1 4.4 25.1 1.0 C4' A:U2 4.6 31.3 1.0 N1 A:U2 4.8 29.0 1.0 O A:HOH139 4.8 58.7 1.0 C5' A:U2 4.9 31.5 1.0 C6 A:U2 4.9 27.8 1.0 C3' A:C1 5.0 28.4 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