Magnesium in PDB 8a1p: Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Bi-D

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Bi-D, PDB code: 8a1p was solved by M.R.Singer, V.E.Pye, N.J.Cook, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.71 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.555, 65.21, 69.673, 90, 100.17, 90
R / Rfree (%)	18.1 / 20.9

The binding sites of Magnesium atom in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Bi-D (pdb code 8a1p). 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 Bi-D, PDB code: 8a1p:
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 Bi-D


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 Bi-D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:50.1 occ:1.00 O B:HOH735 1.8 50.5 1.0 O B:HOH718 1.9 46.5 1.0 OD2 B:ASP116 2.1 51.6 1.0 OD1 B:ASP64 2.1 46.3 1.0 O B:HOH763 2.1 48.4 1.0 O B:HOH720 2.1 52.4 1.0 CG B:ASP116 3.1 51.2 1.0 CG B:ASP64 3.1 48.9 1.0 OD1 B:ASP116 3.4 46.8 1.0 OD2 B:ASP64 3.5 49.7 1.0 O B:HOH712 4.0 47.3 1.0 O B:HOH709 4.2 57.5 1.0 O B:CYS65 4.3 43.6 1.0 O B:HOH719 4.4 55.5 1.0 N B:CYS65 4.4 42.0 1.0 CB B:ASP116 4.4 51.9 1.0 CB B:ASP64 4.5 44.9 1.0 CE2 B:PHE121 4.7 44.1 1.0 CA B:ASP64 4.8 43.2 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 Bi-D


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 Bi-D within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg307 b:41.6 occ:1.00 O D:HOH423 2.1 42.5 1.0 O D:HOH415 2.1 45.2 1.0 O D:HOH410 2.1 46.4 1.0 OD1 D:ASP64 2.1 40.9 1.0 OD2 D:ASP116 2.1 43.2 1.0 O D:HOH463 2.2 45.0 1.0 CG D:ASP64 3.1 46.0 1.0 CG D:ASP116 3.2 48.9 1.0 OD2 D:ASP64 3.4 48.6 1.0 OD1 D:ASP116 3.6 43.7 1.0 O D:HOH418 4.0 44.0 1.0 O D:HOH409 4.1 42.3 1.0 O D:CYS65 4.3 42.4 1.0 O D:HOH406 4.4 45.1 1.0 N D:CYS65 4.4 37.6 1.0 CB D:ASP64 4.5 41.1 1.0 CB D:ASP116 4.5 47.6 1.0 CA D:ASP64 4.8 39.2 1.0 CE2 D:PHE121 4.8 37.7 1.0

M.R.Singer, P.Cherepanov. The Drug-Induced Interface That Drives Hiv-1 Integrase Hypermultimerization and Loss of Function To Be Published 2023.
DOI: 10.1128/MBIO.03560-22