Magnesium in PDB 8t5b: Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110, PDB code: 8t5b was solved by T.Dinh, M.Kvaratskhelia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.72 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.954, 69.984, 63.858, 90, 100.73, 90
R / Rfree (%)	24 / 26.5

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110 (pdb code 8t5b). 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 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110, PDB code: 8t5b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:31.8 occ:0.00 OD2 A:ASP116 2.4 34.0 1.0 OD1 A:ASP64 2.5 32.7 1.0 CG A:ASP64 3.3 34.5 1.0 OD2 A:ASP64 3.3 36.2 1.0 CG A:ASP116 3.4 28.1 1.0 OD1 A:ASP116 3.8 29.2 1.0 H A:CYS65 3.9 42.2 1.0 O A:CYS65 4.4 35.5 1.0 O A:HOH405 4.4 28.9 1.0 O A:HOH402 4.4 39.1 1.0 HB3 A:ASP116 4.5 36.4 1.0 CB A:ASP116 4.5 30.2 1.0 CB A:ASP64 4.7 34.9 1.0 HE2 A:PHE121 4.7 33.6 1.0 N A:CYS65 4.8 35.0 1.0 HA A:ASP64 4.8 38.5 1.0 HB2 A:ASP116 4.8 36.4 1.0 HB2 A:CYS65 4.9 41.6 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Ekc-110 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:40.0 occ:0.00 OD2 B:ASP116 2.3 49.7 1.0 OD1 B:ASP64 2.5 39.8 1.0 CG B:ASP116 3.1 41.7 1.0 OD1 B:ASP116 3.3 41.3 1.0 CG B:ASP64 3.6 38.1 1.0 H B:CYS65 3.6 43.5 1.0 HE2 B:PHE121 3.9 46.7 1.0 OD2 B:ASP64 3.9 37.4 1.0 O B:HOH410 3.9 37.4 1.0 O B:HOH405 4.2 37.3 1.0 HB2 B:CYS65 4.2 37.6 1.0 O B:CYS65 4.4 36.5 1.0 N B:CYS65 4.5 36.0 1.0 CB B:ASP116 4.5 37.7 1.0 HA B:ASP64 4.5 48.3 1.0 HB3 B:ASP116 4.6 45.5 1.0 HB2 B:ASP116 4.7 45.5 1.0 HA3 B:GLY118 4.7 51.8 1.0 CE2 B:PHE121 4.8 38.8 1.0 H B:GLY118 4.8 56.8 1.0 CB B:ASP64 4.9 40.9 1.0 HD2 B:PHE121 4.9 45.5 1.0

T.Dinh, M.Kvaratskhelia. Understanding the Resistance of Y99H and A128T Mutations in Hiv-1 Integrase Against the Effective Anti-Hiv Drugs of STP0404 and BKC11 To Be Published.