Chlorine 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:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl308 b:60.6 occ:1.00 CLA B:WBV308 0.0 60.6 1.0 CAV B:WBV308 1.8 58.5 1.0 CAL B:WBV308 2.7 60.6 1.0 CAK B:WBV308 2.8 60.2 1.0 CB D:TRP132 3.4 65.5 1.0 CE B:MET178 3.6 71.0 1.0 CG D:TRP132 3.7 68.3 1.0 O D:ALA128 3.8 64.0 1.0 CA D:ALA129 3.9 59.4 1.0 CD1 D:TRP132 4.0 69.6 1.0 CAN B:WBV308 4.0 57.9 1.0 CAM B:WBV308 4.1 61.3 1.0 C D:ALA128 4.1 65.7 1.0 N D:ALA129 4.1 62.0 1.0 CG2 C:ILE268 4.3 82.1 1.0 CD2 D:TRP132 4.4 69.2 1.0 CD2 D:LEU102 4.4 57.6 1.0 CD1 D:LEU102 4.5 53.5 1.0 CBA B:WBV308 4.6 60.7 1.0 CG1 C:ILE268 4.6 83.5 1.0 CB D:ALA129 4.6 59.7 1.0 CA D:TRP132 4.8 70.3 1.0 CB D:ALA128 4.8 61.0 1.0 NE1 D:TRP132 4.9 68.3 1.0 C D:ALA129 4.9 59.9 1.0 O D:ALA129 4.9 62.5 1.0 C2 C:EDO501 5.0 82.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1301 b:58.9 occ:1.00 CLA D:WBV1301 0.0 58.9 1.0 CAV D:WBV1301 1.8 54.5 1.0 CAL D:WBV1301 2.7 62.3 1.0 CAK D:WBV1301 2.8 56.0 1.0 CB B:TRP132 3.4 60.0 1.0 CE D:MET178 3.5 60.4 1.0 CG B:TRP132 3.7 59.1 1.0 O B:ALA128 3.7 61.4 1.0 CA B:ALA129 3.8 56.5 1.0 CAN D:WBV1301 4.0 61.9 1.0 CAM D:WBV1301 4.1 57.4 1.0 CD1 B:TRP132 4.1 57.9 1.0 C B:ALA128 4.1 60.6 1.0 N B:ALA129 4.1 56.9 1.0 CG2 A:ILE268 4.4 69.8 1.0 CD1 B:LEU102 4.4 59.3 1.0 CD2 B:TRP132 4.5 56.3 1.0 CB B:ALA129 4.5 57.4 1.0 CD2 B:LEU102 4.5 55.7 1.0 CBA D:WBV1301 4.6 61.2 1.0 CG1 A:ILE268 4.7 83.8 1.0 C B:ALA129 4.8 56.0 1.0 O B:ALA129 4.8 51.8 1.0 CA B:TRP132 4.8 60.5 1.0 CB B:ALA128 4.9 56.7 1.0 NE1 B:TRP132 4.9 66.0 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