Magnesium in PDB 8a1q: Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor STP0404 (Pirmitegravir)

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor STP0404 (Pirmitegravir), PDB code: 8a1q 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)	62.61 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.262, 69.258, 64.106, 90, 102.38, 90
R / Rfree (%)	21.9 / 23.5

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor STP0404 (Pirmitegravir) 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 STP0404 (Pirmitegravir) (pdb code 8a1q). 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 STP0404 (Pirmitegravir), PDB code: 8a1q:
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 STP0404 (Pirmitegravir)


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 STP0404 (Pirmitegravir) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg309 b:57.3 occ:1.00 O B:HOH411 2.0 59.5 1.0 O B:HOH401 2.1 57.1 1.0 OD2 B:ASP116 2.1 66.7 1.0 OD1 B:ASP64 2.1 57.8 1.0 O B:HOH420 2.1 50.2 1.0 O B:HOH437 2.2 67.3 1.0 CG B:ASP116 2.9 58.3 1.0 CG B:ASP64 3.1 60.3 1.0 OD1 B:ASP116 3.2 62.6 1.0 OD2 B:ASP64 3.5 61.3 1.0 O B:HOH403 3.9 59.4 1.0 CB B:ASP116 4.3 60.8 1.0 N B:CYS65 4.3 58.8 1.0 CB B:ASP64 4.4 54.9 1.0 O B:CYS65 4.5 69.2 1.0 O B:HOH402 4.5 71.5 1.0 CE2 B:PHE121 4.6 59.7 1.0 CA B:ASP64 4.7 60.5 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 STP0404 (Pirmitegravir)


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 STP0404 (Pirmitegravir) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1306 b:70.0 occ:1.00 O D:HOH1421 2.0 63.0 1.0 OD2 D:ASP116 2.1 75.0 1.0 OD1 D:ASP64 2.1 64.0 1.0 O D:HOH1417 2.1 67.4 1.0 O D:HOH1418 2.1 60.2 1.0 O D:HOH1445 2.2 77.3 1.0 CG D:ASP116 3.0 67.7 1.0 CG D:ASP64 3.1 65.9 1.0 OD1 D:ASP116 3.4 70.2 1.0 OD2 D:ASP64 3.5 75.2 1.0 O D:HOH1407 4.0 61.8 1.0 O D:HOH1401 4.1 67.5 1.0 N D:CYS65 4.2 57.6 1.0 O D:CYS65 4.3 60.2 1.0 CB D:ASP116 4.4 72.3 1.0 CB D:ASP64 4.4 59.8 1.0 CE2 D:PHE121 4.6 62.8 1.0 CA D:ASP64 4.7 59.3 1.0 C D:ASP64 5.0 62.5 1.0 CA D:CYS65 5.0 54.1 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