Magnesium 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:

Chlorine	(Cl)	1 atom
Sodium	(Na)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hiv-1 Subtype B Genomic Rna Dimerization Initiation Site, PDB code: 1xpe:
Jump to Magnesium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg101 b:64.3 occ:0.62 O A:HOH283 3.5 68.2 1.0 O A:HOH294 3.7 35.4 0.8 O4 A:U3 4.2 42.2 1.0 C5 A:U3 4.8 39.9 1.0 C4 A:U3 4.9 40.9 1.0 O A:HOH254 4.9 70.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg110 b:55.3 occ:0.87 O B:HOH220 2.8 52.5 1.0 O B:HOH298 2.8 32.6 0.9 O B:HOH242 4.1 41.8 1.0 O B:HOH315 4.4 59.8 1.0 O B:HOH267 4.5 90.2 1.0 O B:HOH236 4.6 38.9 0.9 O6 B:G14 4.8 27.2 1.0 N4 B:C13 4.9 26.4 1.0 N4 B:C15 4.9 31.9 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