Magnesium in PDB 1xp7: Hiv-1 Subtype F Genomic Rna Dimerization Initiation Site

The structure of Hiv-1 Subtype F Genomic Rna Dimerization Initiation Site, PDB code: 1xp7 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)	8.00 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	27.380, 116.190, 94.500, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 23

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

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Hiv-1 Subtype F Genomic Rna Dimerization Initiation Site (pdb code 1xp7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hiv-1 Subtype F Genomic Rna Dimerization Initiation Site, PDB code: 1xp7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hiv-1 Subtype F 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 F Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:49.0 occ:1.00 O A:HOH121 2.1 35.7 1.0 O6 A:G7 4.1 35.9 1.0 N7 A:G7 4.3 37.0 1.0 O4 A:U6 4.4 44.0 1.0 O A:HOH113 4.7 20.9 0.9 C5 A:U6 4.8 42.4 1.0 C4 A:U6 4.9 42.4 1.0 C6 A:G7 4.9 35.4 1.0

Magnesium binding site 2 out of 4 in the Hiv-1 Subtype F 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 F Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:82.6 occ:1.00 O A:HOH109 3.4 29.0 1.0 O6 A:G12 3.9 37.0 1.0 O A:HOH118 4.1 51.8 1.0 O4 A:U11 4.3 36.4 1.0 O6 B:G12 4.3 42.7 1.0 O A:HOH117 4.7 44.9 0.9 N4 A:C13 4.7 35.6 1.0 N4 B:C13 4.8 49.9 1.0 O4 B:U11 4.9 47.7 1.0 C6 A:G12 5.0 37.0 1.0 O B:HOH109 5.0 49.7 1.0

Magnesium binding site 3 out of 4 in the Hiv-1 Subtype F 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 3 of Hiv-1 Subtype F Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:65.4 occ:1.00 O B:HOH120 1.9 38.7 0.9 O B:HOH119 3.7 39.8 1.0 O4 B:U6 4.3 42.8 1.0 O6 B:G7 4.5 41.2 1.0 N7 B:G7 4.6 41.0 1.0 C5 B:U6 4.7 40.4 1.0 C4 B:U6 4.7 41.5 1.0

Magnesium binding site 4 out of 4 in the Hiv-1 Subtype F 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 4 of Hiv-1 Subtype F Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:87.7 occ:1.00 O6 B:G19 4.4 41.2 1.0 O6 B:G4 4.8 25.8 1.0 O4 B:U3 4.9 32.7 1.0 N6 B:A18 4.9 40.1 1.0 N7 B:A18 5.0 41.9 1.0 O B:HOH122 5.0 45.0 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