Chlorine 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:

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 Ekc-110 (pdb code 8t5b). 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 Ekc-110, PDB code: 8t5b:
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 Ekc-110


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 Ekc-110 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:40.2 occ:1.00 CL32 A:QD6301 0.0 40.2 1.0 C31 A:QD6301 1.9 33.4 1.0 HE2 A:MET178 2.8 45.7 1.0 HB3 B:TRP132 2.8 39.3 1.0 C33 A:QD6301 2.9 32.6 1.0 C30 A:QD6301 2.9 32.6 1.0 HB2 B:TRP132 2.9 39.3 1.0 HD21 B:LEU102 2.9 44.3 1.0 HA B:ALA129 3.0 42.7 1.0 H331 A:QD6301 3.0 39.4 1.0 HE3 A:MET178 3.0 45.7 1.0 H301 A:QD6301 3.0 39.3 1.0 CB B:TRP132 3.1 32.6 1.0 CE A:MET178 3.3 37.9 1.0 CG B:TRP132 3.3 36.2 1.0 HD11 B:LEU102 3.4 45.9 1.0 HE1 A:MET178 3.5 45.7 1.0 CD1 B:TRP132 3.8 36.5 1.0 CD2 B:LEU102 3.8 36.7 1.0 CD2 B:TRP132 3.9 35.9 1.0 CA B:ALA129 3.9 35.4 1.0 HG23 D:ILE268 3.9 46.7 1.0 HD22 B:LEU102 4.0 44.3 1.0 HD1 B:TRP132 4.0 44.0 1.0 O B:ALA128 4.1 31.6 1.0 CD1 B:LEU102 4.2 38.1 1.0 HD13 B:LEU102 4.2 45.9 1.0 C34 A:QD6301 4.2 34.1 1.0 C29 A:QD6301 4.2 31.9 1.0 N B:ALA129 4.4 31.8 1.0 HD23 B:LEU102 4.4 44.3 1.0 HE3 B:TRP132 4.4 40.4 1.0 HG21 D:ILE268 4.4 46.7 1.0 CE3 B:TRP132 4.5 33.5 1.0 C B:ALA128 4.5 34.3 1.0 HB2 B:ALA129 4.5 33.7 1.0 HG2 A:MET178 4.5 44.5 1.0 HD12 D:ILE268 4.5 42.1 1.0 H B:TRP132 4.5 40.9 1.0 NE1 B:TRP132 4.6 36.1 1.0 CG2 D:ILE268 4.6 38.8 1.0 CG B:LEU102 4.6 36.4 1.0 CA B:TRP132 4.6 36.4 1.0 CE2 B:TRP132 4.6 35.8 1.0 O B:ALA129 4.6 31.9 1.0 CB B:ALA129 4.7 27.9 1.0 HB1 B:ALA128 4.7 39.5 1.0 C28 A:QD6301 4.7 33.0 1.0 HB1 B:ALA129 4.7 33.7 1.0 C B:ALA129 4.8 30.4 1.0 HG22 D:ILE268 4.9 46.7 1.0 SD A:MET178 4.9 36.1 1.0 H B:ALA129 4.9 38.4 1.0 HG B:LEU102 4.9 43.9 1.0 HG23 A:THR174 5.0 35.0 1.0 HG3 A:MET178 5.0 44.5 1.0 HD12 B:LEU102 5.0 45.9 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 Ekc-110


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 Ekc-110 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:38.0 occ:1.00 CL32 B:QD6301 0.0 38.0 1.0 C31 B:QD6301 1.9 32.8 1.0 HB3 A:TRP132 2.8 35.2 1.0 HE2 B:MET178 2.8 40.2 1.0 C33 B:QD6301 2.9 33.3 1.0 C30 B:QD6301 2.9 30.4 1.0 HA A:ALA129 2.9 38.2 1.0 HD21 A:LEU102 2.9 40.2 1.0 HB2 A:TRP132 2.9 35.2 1.0 H331 B:QD6301 3.0 40.2 1.0 H301 B:QD6301 3.0 36.7 1.0 CB A:TRP132 3.1 29.1 1.0 HE3 B:MET178 3.3 40.2 1.0 HD11 A:LEU102 3.3 44.6 1.0 CG A:TRP132 3.4 28.7 1.0 CE B:MET178 3.4 33.3 1.0 HE1 B:MET178 3.7 40.2 1.0 CA A:ALA129 3.8 31.7 1.0 CD2 A:LEU102 3.9 33.3 1.0 CD1 A:TRP132 3.9 34.0 1.0 CD2 A:TRP132 3.9 30.2 1.0 O A:ALA128 4.0 30.0 1.0 CD1 A:LEU102 4.1 37.0 1.0 HG23 C:ILE268 4.1 39.4 1.0 HD1 A:TRP132 4.1 41.0 1.0 HD13 A:LEU102 4.1 44.6 1.0 HG21 C:ILE268 4.2 39.4 1.0 HD22 A:LEU102 4.2 40.2 1.0 C34 B:QD6301 4.2 31.1 1.0 C29 B:QD6301 4.2 31.1 1.0 N A:ALA129 4.3 31.9 1.0 HE3 A:TRP132 4.3 40.0 1.0 C A:ALA128 4.4 29.7 1.0 HD23 A:LEU102 4.4 40.2 1.0 CE3 A:TRP132 4.4 33.1 1.0 HD12 C:ILE268 4.4 44.4 1.0 HB2 A:ALA129 4.5 36.8 1.0 H A:TRP132 4.5 37.4 1.0 HG2 B:MET178 4.5 38.3 1.0 CG A:LEU102 4.5 36.3 1.0 O A:ALA129 4.6 26.6 1.0 CG2 C:ILE268 4.6 32.6 1.0 CA A:TRP132 4.6 32.2 1.0 CB A:ALA129 4.6 30.5 1.0 HB1 A:ALA128 4.6 37.7 1.0 HB1 A:ALA129 4.7 36.8 1.0 NE1 A:TRP132 4.7 37.4 1.0 C A:ALA129 4.7 25.2 1.0 CE2 A:TRP132 4.7 30.6 1.0 C28 B:QD6301 4.7 32.0 1.0 HG A:LEU102 4.8 43.7 1.0 H A:ALA129 4.8 38.5 1.0 HD12 A:LEU102 4.9 44.6 1.0 HG22 C:ILE268 5.0 39.4 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.