Magnesium 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:

Sodium

(Na)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Hiv-1 Subtype A Genomic Rna Dimerization Initiation Site, PDB code: 1xpf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Hiv-1 Subtype A 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 A Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:61.9 occ:1.00 O6 A:G7 3.9 30.4 1.0 O4 A:U6 4.0 39.0 1.0 O A:HOH143 4.1 40.9 1.0 C4 A:U6 4.7 42.0 1.0 N7 A:G7 4.9 32.4 1.0 O A:HOH151 4.9 43.3 1.0 C6 A:G7 4.9 33.1 1.0 C5 A:U6 4.9 41.9 1.0 O A:HOH152 5.0 43.6 1.0

Magnesium binding site 2 out of 3 in the Hiv-1 Subtype A 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 A Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:37.1 occ:0.70 OP1 A:G12 2.3 35.1 1.0 P A:G12 3.7 33.1 1.0 O5' A:G12 4.3 33.1 1.0 C5' A:G12 4.3 33.3 1.0 OP2 A:G12 4.5 35.9 1.0 OP2 A:C13 4.7 34.9 1.0 O3' A:U11 4.8 31.1 1.0 O A:HOH130 5.0 61.3 1.0

Magnesium binding site 3 out of 3 in the Hiv-1 Subtype A 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 A Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:47.9 occ:1.00 O2' A:G9 3.7 31.0 1.0 OP1 B:G10 3.7 34.7 1.0 C6 A:SPM108 3.7 58.9 0.8 OP1 A:G10 3.8 31.2 1.0 C3' B:G9 3.8 30.6 1.0 C2' B:G9 3.9 30.8 1.0 O2' B:G9 4.0 31.0 1.0 C2' A:G9 4.1 28.3 1.0 C3' A:G9 4.2 29.1 1.0 O5' B:G9 4.3 31.0 1.0 C8 A:SPM108 4.6 57.0 0.8 O A:HOH124 4.6 48.3 1.0 O3' B:G9 4.7 33.6 1.0 N5 A:SPM108 4.7 59.1 0.8 O3' A:G9 4.8 29.4 1.0 C7 A:SPM108 4.8 58.8 0.8 P B:G10 4.8 34.3 1.0 P A:G10 4.8 28.8 1.0 C5' B:G9 4.9 28.5 1.0 O B:HOH118 4.9 59.8 1.0 C4' B:G9 4.9 29.8 1.0 N10 A:SPM108 5.0 56.4 0.8

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