Iodine in PDB 6vka: Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand

The structure of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand, PDB code: 6vka was solved by M.A.Gorman, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.30 / 1.86
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	46.302, 46.302, 138.051, 90, 90, 90
R / Rfree (%)	14.5 / 21.2

The binding sites of Iodine atom in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand (pdb code 6vka). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand, PDB code: 6vka:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:38.4 occ:1.00 H A:LYS173 3.1 19.8 1.0 HE3 A:LYS71 3.1 41.4 1.0 HB3 A:LEU172 3.3 26.4 1.0 HZ2 A:LYS71 3.3 51.9 1.0 HD3 A:LYS71 3.4 33.9 1.0 HB3 A:LYS173 3.4 27.7 1.0 HG2 A:LYS173 3.4 17.0 1.0 HE3 A:LYS173 3.6 49.8 1.0 H A:LEU172 3.6 26.3 1.0 HB3 A:HIS171 3.7 24.7 1.0 O A:HOH451 3.7 22.7 1.0 CE A:LYS71 3.8 34.5 1.0 HD2 A:HIS171 3.8 41.0 1.0 N A:LYS173 3.8 16.5 1.0 NZ A:LYS71 3.9 43.2 1.0 CD A:LYS71 3.9 28.2 1.0 N A:LEU172 4.1 21.9 1.0 HD2 A:LYS71 4.1 33.9 1.0 HG11 A:VAL88 4.1 40.7 1.0 HG21 A:VAL88 4.1 17.9 1.0 CB A:LYS173 4.1 23.1 1.0 CG A:LYS173 4.1 14.2 1.0 HZ1 A:LYS71 4.2 51.9 1.0 CB A:LEU172 4.2 22.0 1.0 O A:HOH431 4.4 26.0 1.0 CE A:LYS173 4.4 41.5 1.0 CA A:LEU172 4.5 21.4 1.0 CB A:HIS171 4.5 20.6 1.0 CA A:LYS173 4.6 20.6 1.0 HD2 A:LYS173 4.6 33.2 1.0 CD2 A:HIS171 4.6 34.2 1.0 HB2 A:LEU172 4.6 26.4 1.0 C A:LEU172 4.6 12.2 1.0 CD A:LYS173 4.6 27.7 1.0 HA A:HIS171 4.6 27.4 1.0 HE2 A:LYS71 4.7 41.4 1.0 HZ3 A:LYS71 4.7 51.9 1.0 HE2 A:LYS173 4.7 49.8 1.0 HD23 A:LEU172 4.8 28.4 1.0 C A:HIS171 4.8 19.7 1.0 HB A:VAL88 4.9 27.3 1.0 CA A:HIS171 4.9 22.8 1.0 HA A:LYS173 4.9 24.7 1.0 CG1 A:VAL88 4.9 33.9 1.0 HB2 A:LYS173 4.9 27.7 1.0 CG A:HIS171 4.9 33.0 1.0 HG3 A:LYS173 4.9 17.0 1.0 CG2 A:VAL88 5.0 14.9 1.0

Iodine binding site 2 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:23.0 occ:1.00 H A:GLY70 2.8 31.4 1.0 HB3 A:HIS67 3.1 27.3 1.0 HA2 A:GLY70 3.3 24.1 1.0 N A:GLY70 3.5 26.1 1.0 O A:HOH436 3.6 20.7 1.0 HA A:LEU68 3.9 30.0 1.0 HB2 A:HIS67 3.9 27.3 1.0 CB A:HIS67 3.9 22.8 1.0 CA A:GLY70 3.9 20.1 1.0 H A:GLU69 4.1 28.3 1.0 N A:LEU68 4.1 17.4 1.0 H A:LYS71 4.1 26.4 1.0 C A:HIS67 4.1 19.6 1.0 N A:GLU69 4.2 23.6 1.0 C A:LEU68 4.2 20.4 1.0 CA A:LEU68 4.3 25.0 1.0 H A:LEU68 4.3 20.9 1.0 O A:HIS67 4.4 23.9 1.0 CA A:HIS67 4.6 20.9 1.0 N A:LYS71 4.7 22.0 1.0 C A:GLU69 4.7 20.1 1.0 HA3 A:GLY70 4.7 24.1 1.0 O A:HOH434 4.7 27.4 1.0 C A:GLY70 4.7 21.5 1.0 O A:LEU68 4.8 25.5 1.0 O A:LYS71 4.9 17.0 1.0 CA A:GLU69 4.9 24.0 1.0 HA A:HIS67 4.9 25.0 1.0 HA A:GLU69 5.0 28.8 1.0

Iodine binding site 3 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:I309 b:30.5 occ:1.00 HA A:LYS186 3.2 15.2 1.0 N A:ARG187 3.6 22.4 1.0 HG3 A:LYS186 3.7 25.6 1.0 CA A:LYS186 4.1 12.7 1.0 CB A:ARG187 4.2 27.9 1.0 CG A:ARG187 4.2 24.9 1.0 HG2 A:LYS186 4.2 25.6 1.0 O A:LYS185 4.3 16.6 1.0 CG A:LYS186 4.3 21.3 1.0 C A:LYS186 4.3 28.6 1.0 CD A:ARG187 4.4 17.6 1.0 CA A:ARG187 4.5 20.9 1.0 CB A:LYS186 4.7 20.4 1.0 HB2 A:LYS186 5.0 24.5 1.0

Iodine binding site 4 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:I301 b:36.9 occ:0.90 HG3 B:LYS173 2.6 33.2 1.0 HD3 B:LYS173 2.9 29.3 1.0 H B:LYS173 2.9 20.7 1.0 HE2 B:LYS71 3.1 45.6 1.0 HB3 B:LEU172 3.3 25.5 1.0 CG B:LYS173 3.4 27.7 1.0 O B:HOH441 3.5 17.0 1.0 CD B:LYS173 3.5 24.4 1.0 HB3 B:HIS171 3.6 19.5 1.0 HB2 B:LYS173 3.6 21.9 1.0 O B:HOH439 3.7 24.7 1.0 N B:LYS173 3.7 17.2 1.0 H B:LEU172 3.7 20.7 1.0 HD2 B:LYS173 3.9 29.3 1.0 CB B:LYS173 4.0 18.3 1.0 HZ3 B:LYS71 4.0 44.8 1.0 CE B:LYS71 4.0 38.0 1.0 HG11 B:VAL88 4.0 35.3 1.0 N B:LEU172 4.1 17.3 1.0 CB B:LEU172 4.2 21.3 1.0 HG2 B:LYS173 4.2 33.2 1.0 HG2 B:LYS71 4.2 42.9 1.0 HG21 B:VAL88 4.3 22.1 1.0 HD3 B:LYS71 4.4 41.8 1.0 CA B:LYS173 4.4 17.6 1.0 HD2 B:HIS171 4.5 27.6 1.0 CB B:HIS171 4.5 16.3 1.0 HA B:HIS171 4.5 24.8 1.0 CA B:LEU172 4.5 15.8 1.0 NZ B:LYS71 4.5 37.4 1.0 HD23 B:LEU172 4.6 25.4 1.0 HB B:VAL88 4.6 28.9 1.0 HB2 B:LEU172 4.6 25.5 1.0 C B:LEU172 4.6 12.2 1.0 HE3 B:LYS71 4.6 45.6 1.0 HG12 B:VAL88 4.7 35.3 1.0 CD B:LYS71 4.7 34.8 1.0 CG1 B:VAL88 4.7 29.4 1.0 C B:HIS171 4.7 19.5 1.0 HE2 B:LYS173 4.8 29.9 1.0 HA B:LYS173 4.8 21.1 1.0 CE B:LYS173 4.8 24.9 1.0 CA B:HIS171 4.8 20.6 1.0 HB3 B:LYS173 4.8 21.9 1.0 CG B:LYS71 4.9 35.7 1.0 HZ1 B:LYS71 5.0 44.8 1.0

Iodine binding site 5 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:31.1 occ:1.00 HA3 B:GLY82 3.1 21.6 1.0 O B:HOH405 3.4 25.1 1.0 HE1 B:HIS183 3.4 18.7 1.0 HD2 B:LYS188 3.5 23.1 1.0 HE2 B:HIS183 3.5 23.1 1.0 CE1 B:HIS183 3.9 15.6 1.0 HD3 B:LYS188 3.9 23.1 1.0 NE2 B:HIS183 3.9 19.3 1.0 HB2 B:ALA196 4.0 16.5 1.0 HG2 B:LYS188 4.0 21.6 1.0 CA B:GLY82 4.1 18.0 1.0 CD B:LYS188 4.1 19.2 1.0 HB3 B:LYS188 4.2 23.4 1.0 HA2 B:GLY82 4.3 21.6 1.0 O B:GLY82 4.3 15.1 1.0 CG B:LYS188 4.5 18.0 1.0 O B:SER81 4.5 16.2 1.0 HA B:LYS188 4.6 26.2 1.0 C B:GLY82 4.6 8.1 1.0 CB B:LYS188 4.7 19.5 1.0 CE B:MET154 4.7 27.5 1.0 O B:HOH440 4.9 40.1 1.0 HZ1 B:LYS186 4.9 24.1 1.0 CB B:ALA196 4.9 13.7 1.0 HZ2 B:LYS186 5.0 24.1 1.0

Iodine binding site 6 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:I308 b:43.4 occ:1.00 H B:GLY70 2.7 40.4 1.0 HB3 B:HIS67 3.4 42.6 1.0 HB2 B:HIS67 3.4 42.6 1.0 HA B:LEU68 3.4 33.5 1.0 N B:GLY70 3.6 33.7 1.0 HA2 B:GLY70 3.6 32.6 1.0 H B:GLU69 3.8 33.4 1.0 N B:LEU68 3.8 28.6 1.0 CB B:HIS67 3.8 35.5 1.0 CA B:LEU68 3.9 27.9 1.0 N B:GLU69 3.9 27.8 1.0 C B:LEU68 4.0 26.3 1.0 C B:HIS67 4.0 24.5 1.0 H B:LEU68 4.0 34.3 1.0 CA B:GLY70 4.1 27.1 1.0 O B:HIS67 4.3 27.4 1.0 CA B:HIS67 4.5 35.7 1.0 C B:GLU69 4.6 29.0 1.0 O B:LEU68 4.7 33.8 1.0 H B:LYS71 4.7 42.8 1.0 CA B:GLU69 4.7 26.1 1.0 HA B:GLU69 4.7 31.3 1.0 HA3 B:GLY70 4.8 32.6 1.0 HA B:HIS67 4.9 42.9 1.0 O B:HOH434 4.9 27.4 1.0 HD12 B:LEU68 4.9 39.8 1.0

M.Scanlon, M.A.Gorman. Hiv Integrase Core Domain (in) in Complex with Dimeric Spanning Inhibitor To Be Published.