Magnesium in PDB 1y99: Hiv-1 Subtype A Dis Rna Duplex

The structure of Hiv-1 Subtype A Dis Rna Duplex, PDB code: 1y99 was solved by E.Ennifar, M.Yusupov, P.Walter, R.Marquet, B.Ehresmann, C.Ehresmann, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.97 / 2.40
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	45.698, 31.422, 51.188, 90.00, 115.82, 90.00
R / Rfree (%)	22.5 / 23.8

The binding sites of Magnesium atom in the Hiv-1 Subtype A Dis Rna Duplex (pdb code 1y99). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Hiv-1 Subtype A Dis Rna Duplex, PDB code: 1y99:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Hiv-1 Subtype A Dis Rna Duplex


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 Dis Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg700 b:54.2 occ:1.00 O B:HOH138 3.4 45.3 1.0 O A:HOH175 4.2 39.6 1.0 O B:HOH115 4.3 29.6 1.0 O B:HOH111 4.4 45.2 1.0 O6 A:G7 4.5 25.6 0.5 O B:HOH174 4.5 56.3 1.0 O4 A:U6 4.7 43.6 1.0 N7 A:G7 5.0 26.5 0.5

Magnesium binding site 2 out of 7 in the Hiv-1 Subtype A Dis Rna Duplex


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 Dis Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg710 b:58.7 occ:1.00 O A:HOH167 2.5 52.6 1.0 O A:HOH172 3.0 56.4 1.0 O B:HOH145 3.0 47.8 1.0 O6 A:G12 3.1 36.4 1.0 O B:HOH108 3.2 46.8 1.0 O6 B:G12 4.0 27.7 1.0 O A:HOH156 4.2 59.0 1.0 C6 A:G12 4.2 32.3 1.0 O4 A:U11 4.3 33.5 1.0 N4 A:C13 4.3 33.9 1.0 N4 B:C13 4.3 28.1 1.0 O B:HOH120 4.6 33.7 1.0 N7 A:G12 4.8 33.6 1.0 C5 A:G12 4.9 31.6 1.0

Magnesium binding site 3 out of 7 in the Hiv-1 Subtype A Dis Rna Duplex


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 Dis Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg720 b:48.6 occ:1.00 O A:HOH128 2.4 43.1 1.0 O6 A:G4 2.5 36.8 1.0 N4 B:C20 3.0 38.8 1.0 O6 B:G19 3.2 42.3 1.0 O4 A:U3 3.3 34.8 1.0 C6 A:G4 3.7 37.5 1.0 O B:HOH157 3.7 53.8 1.0 C6 B:G19 4.2 43.1 1.0 N6 B:A21 4.2 37.5 1.0 C4 B:C20 4.2 42.6 1.0 N4 A:C5 4.3 36.5 1.0 C4 A:U3 4.3 35.8 1.0 C5 A:G4 4.5 38.6 1.0 N7 A:G4 4.6 39.1 1.0 N3 B:C20 4.6 43.5 1.0 N1 A:G4 4.7 41.1 1.0 C5 B:G19 4.9 41.2 1.0 C6 B:A21 5.0 38.6 1.0

Magnesium binding site 4 out of 7 in the Hiv-1 Subtype A Dis Rna Duplex


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 A Dis Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg760 b:37.2 occ:1.00 O A:HOH122 2.1 40.5 1.0 O A:HOH762 2.1 32.1 1.0 O A:HOH761 2.1 36.9 1.0 O A:HOH763 2.3 50.3 1.0 OP2 A:A8 2.4 33.9 0.5 OP2 A:A8 2.5 38.9 0.5 N7 A:G9 2.6 36.9 0.5 N7 A:G9 2.6 36.7 0.5 C8 A:G9 3.3 38.8 0.5 C8 A:G9 3.3 38.1 0.5 C5 A:G9 3.6 38.1 0.5 C5 A:G9 3.7 37.3 0.5 P A:A8 3.7 34.0 0.5 P A:A8 3.8 37.9 0.5 O A:HOH117 4.0 45.3 1.0 O6 A:G9 4.0 35.3 0.5 O5' A:A8 4.0 43.2 0.5 O5' A:A8 4.0 40.4 0.5 C5' A:A8 4.1 43.5 0.5 O6 A:G9 4.1 32.2 0.5 C6 A:G9 4.1 36.8 0.5 OP2 A:G9 4.3 40.2 0.5 C6 A:G9 4.3 35.5 0.5 O3' A:G7 4.5 37.5 0.5 N9 A:G9 4.5 38.4 0.5 C2' A:G7 4.6 33.8 0.5 N9 A:G9 4.6 39.7 0.5 N7 A:G10 4.6 35.0 1.0 O3' A:G7 4.7 36.0 0.5 C4 A:G9 4.7 38.8 0.5 C3' A:G7 4.7 34.4 0.5 OP1 A:A8 4.7 38.1 0.5 C4 A:G9 4.8 38.7 0.5 C3' A:G7 4.8 34.0 0.5 C2' A:G7 4.9 33.4 0.5 OP1 A:A8 5.0 40.8 0.5 O B:HOH174 5.0 56.3 1.0

Magnesium binding site 5 out of 7 in the Hiv-1 Subtype A Dis Rna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hiv-1 Subtype A Dis Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg730 b:54.5 occ:1.00 O A:HOH149 2.6 52.7 1.0 O A:HOH129 2.7 34.7 1.0 O6 B:G4 2.9 40.1 1.0 O4 B:U3 3.3 40.3 1.0 O A:HOH106 3.5 37.2 1.0 C4 B:U3 4.0 40.0 1.0 C6 B:G4 4.0 37.0 1.0 N7 B:G4 4.2 36.3 1.0 C5 B:U3 4.2 39.6 1.0 N4 A:C20 4.3 31.0 1.0 C5 B:G4 4.5 37.0 1.0 O6 A:G19 4.5 29.4 1.0 N4 B:C5 4.5 33.8 1.0 O B:HOH112 4.7 42.8 1.0 O A:HOH121 4.9 56.0 1.0

Magnesium binding site 6 out of 7 in the Hiv-1 Subtype A Dis Rna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Hiv-1 Subtype A Dis Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg740 b:63.3 occ:1.00 O A:HOH142 3.7 56.3 1.0 O6 B:G7 4.4 36.5 1.0 N7 B:G7 4.5 39.3 1.0 O4 B:U6 4.6 32.7 1.0 C5 B:U6 4.8 29.5 1.0 O A:HOH177 4.9 66.2 1.0 C4 B:U6 5.0 34.2 1.0

Magnesium binding site 7 out of 7 in the Hiv-1 Subtype A Dis Rna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Hiv-1 Subtype A Dis Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg750 b:75.4 occ:1.00 OP1 B:G9 2.7 48.5 1.0 OP1 A:G9 2.9 39.8 0.5 OP2 B:G10 3.1 44.5 1.0 OP1 B:G10 3.2 48.6 1.0 P B:G10 3.5 45.5 1.0 P A:G9 3.8 39.1 0.5 O3' B:G9 3.9 44.7 1.0 O3' A:A8 4.0 44.2 0.5 P B:G9 4.1 45.9 1.0 OP2 A:G9 4.3 40.2 0.5 OP2 A:G9 4.3 44.4 0.5 O3' A:A8 4.3 45.6 0.5 C5' B:G9 4.4 41.4 1.0 O5' B:G9 4.5 45.7 1.0 C3' B:G9 4.7 43.5 1.0 O3' B:A8 4.9 44.8 1.0

E.Ennifar, M.Yusupov, P.Walter, R.Marquet, B.Ehresmann, C.Ehresmann, P.Dumas. The Crystal Structure of the Dimerization Initiation Site of Genomic Hiv-1 Rna Reveals An Extended Duplex with Two Adenine Bulges Structure Fold.Des. V. 7 1439 1999.
ISSN: ISSN 0969-2126
PubMed: 10574792
DOI: 10.1016/S0969-2126(00)80033-7