Magnesium in PDB 5oi2: Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1

The structure of Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1, PDB code: 5oi2 was solved by M.Ruff, R.Benarous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.37 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.194, 72.194, 65.935, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 22

The structure of Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Magnesium atom in the Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1 (pdb code 5oi2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1, PDB code: 5oi2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:60.6 occ:1.00 OD1 A:ASP64 2.7 87.5 1.0 N A:CAS65 3.1 39.0 1.0 ND2 A:ASN120 3.3 48.0 1.0 CA A:ASP64 3.5 42.5 1.0 CG A:ASP64 3.6 68.8 1.0 CB A:ASP64 3.6 48.5 1.0 O A:HOH410 3.8 68.0 1.0 O A:CAS65 3.8 45.1 1.0 C A:ASP64 3.8 41.4 1.0 CB A:ASN117 3.9 36.1 1.0 AS A:CAS65 4.1 56.3 1.0 CA A:CAS65 4.2 45.6 1.0 CG A:ASN120 4.3 49.1 1.0 CB A:CAS65 4.4 51.3 1.0 OG1 A:THR115 4.4 34.4 1.0 C A:CAS65 4.5 46.6 1.0 N A:ASN117 4.5 33.9 1.0 OD1 A:ASN120 4.5 52.2 1.0 CE2 A:CAS65 4.5 49.0 1.0 OD2 A:ASP64 4.8 69.7 1.0 O A:LEU63 4.8 41.4 1.0 CA A:ASN117 4.8 36.0 1.0 N A:ASP64 4.8 38.8 1.0 ND2 A:ASN117 4.9 40.3 1.0 OE1 A:GLU92 4.9 71.5 1.0 CG A:ASN117 5.0 41.7 1.0

Magnesium binding site 2 out of 4 in the Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:65.1 occ:1.00 O A:PRO109 2.6 54.7 1.0 O A:PRO58 2.8 46.6 1.0 NE1 A:TRP61 3.0 36.7 1.0 C A:PRO109 3.4 46.5 1.0 CD1 A:ILE204 3.5 58.1 1.0 CA A:GLY59 3.6 50.1 1.0 CD A:PRO109 3.7 42.6 1.0 CG A:PRO109 3.7 43.1 1.0 C A:PRO58 3.8 55.1 1.0 CE1 A:HIS78 3.9 35.3 1.0 CE2 A:TRP61 3.9 33.8 1.0 N A:PRO109 3.9 42.1 1.0 CD1 A:TRP61 4.0 34.1 1.0 ND1 A:HIS78 4.0 38.6 1.0 CA A:PRO109 4.1 40.8 1.0 N A:GLY59 4.1 47.6 1.0 CZ2 A:TRP61 4.2 35.7 1.0 N A:VAL110 4.2 41.5 1.0 C A:GLY59 4.2 46.2 1.0 CB A:TRP108 4.3 36.5 1.0 CB A:PRO109 4.3 45.7 1.0 CA A:VAL110 4.4 38.1 1.0 O A:GLY59 4.6 40.5 1.0 C A:TRP108 4.7 40.4 1.0 CG1 A:ILE204 4.8 53.6 1.0 N A:ILE60 4.9 40.8 1.0 NE2 A:HIS78 5.0 37.7 1.0

Magnesium binding site 3 out of 4 in the Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:73.1 occ:1.00 O A:ILE84 2.9 30.0 1.0 OH A:TYR83 3.2 38.1 1.0 CG1 A:VAL180 3.3 29.9 1.0 OD1 A:ASN184 3.3 38.7 1.0 CG A:GLU85 3.6 50.3 1.0 O A:HOH440 3.6 31.2 1.0 CZ A:TYR83 3.6 41.8 1.0 C A:ILE84 4.0 34.0 1.0 CE2 A:TYR83 4.0 37.3 1.0 CA A:GLU85 4.0 43.1 1.0 CD A:GLU85 4.0 55.4 1.0 OE2 A:GLU85 4.3 45.2 1.0 CB A:GLU85 4.3 44.3 1.0 CE1 A:TYR83 4.4 35.8 1.0 N A:GLU85 4.4 34.3 1.0 CG A:ASN184 4.6 33.7 1.0 OE1 A:GLU85 4.7 61.3 1.0 CB A:VAL180 4.8 31.1 1.0 CD2 A:TYR83 5.0 36.8 1.0

Magnesium binding site 4 out of 4 in the Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dissociation of Biochemical and Antiretroviral Activities of Integrase-Ledgf Allosteric Inhibitors Revealed By Resistance of A125 Polymorphic Hiv-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:78.4 occ:1.00 OE1 A:GLN177 2.7 37.9 1.0 O A:LYS173 3.1 32.6 1.0 N A:VAL88 3.3 37.6 1.0 CA A:LYS173 3.5 36.2 1.0 CB A:LYS173 3.5 38.6 1.0 CD A:GLN177 3.6 30.7 1.0 CG1 A:VAL176 3.7 34.5 1.0 C A:LYS173 3.7 33.3 1.0 CA A:GLU87 3.7 39.2 1.0 CG A:GLN177 3.8 32.3 1.0 CB A:VAL176 3.9 35.5 1.0 CG2 A:VAL88 3.9 39.7 1.0 C A:GLU87 4.0 38.1 1.0 CB A:VAL88 4.1 41.2 1.0 CA A:VAL88 4.3 43.0 1.0 O A:ALA86 4.4 40.2 1.0 N A:GLU87 4.5 40.6 1.0 N A:GLN177 4.6 33.9 1.0 CG A:LYS173 4.6 40.1 1.0 OE1 A:GLU87 4.6 83.0 1.0 O A:HOH401 4.7 65.8 1.0 C A:ALA86 4.7 39.7 1.0 CB A:GLU87 4.8 45.5 1.0 NE2 A:GLN177 4.8 35.6 1.0 CG2 A:VAL176 4.8 35.6 1.0 N A:LYS173 4.9 34.9 1.0 N A:THR174 5.0 30.5 1.0

D.Bonnard, E.Le Rouzic, S.Eiler, C.Amadori, I.Orlov, J.M.Bruneau, J.Brias, J.Barbion, F.Chevreuil, D.Spehner, S.Chasset, B.Ledoussal, F.Moreau, A.Saib, B.P.Klaholz, S.Emiliani, M.Ruff, A.Zamborlini, R.Benarous. Structure-Function Analyses Unravel Distinct Effects of Allosteric Inhibitors of Hiv-1 Integrase on Viral Maturation and Integration. J. Biol. Chem. V. 293 6172 2018.
ISSN: ESSN 1083-351X
PubMed: 29507092
DOI: 10.1074/JBC.M117.816793