Cadmium in PDB 3vqq: Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine

The structure of Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine, PDB code: 3vqq was solved by J.Wielens, D.K.Chalmers, M.W.Parker, M.J.Scanlon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.18 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.399, 61.681, 81.893, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22

The binding sites of Cadmium atom in the Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine (pdb code 3vqq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine, PDB code: 3vqq:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:19.1 occ:0.82 OE1 A:GLU92 2.2 18.4 1.0 NE2 A:HIS67 2.3 21.0 1.0 SG A:CYS65 2.5 18.9 1.0 O A:HOH447 2.6 23.9 1.0 CD A:GLU92 3.1 26.6 1.0 CE1 A:HIS67 3.2 19.5 1.0 OE2 A:GLU92 3.2 25.7 1.0 CD2 A:HIS67 3.3 20.8 1.0 CB A:CYS65 3.4 19.5 1.0 CD A:CD302 3.6 27.3 1.0 ND1 A:HIS67 4.4 20.2 1.0 CG A:HIS67 4.4 20.9 1.0 CG A:GLU92 4.5 23.2 1.0 O A:HOH411 4.5 19.7 1.0 CA A:CYS65 4.8 20.9 1.0 C A:CYS65 5.0 22.7 1.0

Cadmium binding site 2 out of 4 in the Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:27.3 occ:1.00 OD2 A:ASP116 2.2 25.1 1.0 O A:HOH452 2.4 22.4 1.0 SG A:CYS65 2.5 18.9 1.0 OE2 A:GLU92 2.6 25.7 1.0 O A:HOH402 2.7 16.7 1.0 CG A:ASP116 3.2 21.8 1.0 CB A:CYS65 3.2 19.5 1.0 OD1 A:ASP116 3.3 19.6 1.0 CD A:CD301 3.6 19.1 0.8 CD A:GLU92 3.7 26.6 1.0 OE1 A:GLU92 4.1 18.4 1.0 O A:HOH411 4.2 19.7 1.0 N A:CYS65 4.2 25.1 1.0 CA A:CYS65 4.4 20.9 1.0 OD1 A:ASN120 4.6 25.6 1.0 CB A:ASP116 4.6 21.0 1.0 O A:HOH405 4.7 21.6 1.0 O A:HOH447 4.8 23.9 1.0 CE2 A:PHE121 4.9 26.4 1.0 OD1 A:ASP64 4.9 55.7 1.0 CG A:GLU92 4.9 23.2 1.0

Cadmium binding site 3 out of 4 in the Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:38.4 occ:1.00 OE2 B:GLU92 2.3 39.4 1.0 O B:HOH422 2.5 31.2 1.0 OD2 B:ASP116 2.6 32.0 1.0 SG B:CYS65 2.6 32.0 1.0 O B:HOH407 2.7 31.1 1.0 CD B:GLU92 3.2 44.1 1.0 OE1 B:GLU92 3.4 37.5 1.0 CD B:CD302 3.4 43.8 1.0 CG B:ASP116 3.5 32.8 1.0 CB B:CYS65 3.6 35.6 1.0 OD1 B:ASP116 3.7 32.2 1.0 CE2 B:PHE121 4.2 28.8 1.0 N B:CYS65 4.3 34.9 1.0 O B:HOH425 4.3 37.4 1.0 OD1 B:ASN120 4.4 37.2 1.0 O B:HOH434 4.6 38.5 1.0 CG B:GLU92 4.6 37.1 1.0 CA B:CYS65 4.6 30.6 1.0 ND2 B:ASN120 4.9 27.1 1.0 CB B:ASP116 4.9 29.7 1.0

Cadmium binding site 4 out of 4 in the Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hiv-1 Integrase Core Domain in Complex with 2,1,3-Benzothiadiazol-4- Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:43.8 occ:1.00 NE2 B:HIS67 2.3 30.1 1.0 OE1 B:GLU92 2.4 37.5 1.0 SG B:CYS65 2.6 32.0 1.0 O B:HOH434 2.7 38.5 1.0 CE1 B:HIS67 3.0 32.0 1.0 CD B:CD301 3.4 38.4 1.0 CD2 B:HIS67 3.4 32.5 1.0 CD B:GLU92 3.5 44.1 1.0 CB B:CYS65 3.7 35.6 1.0 OE2 B:GLU92 3.9 39.4 1.0 O B:HOH425 4.1 37.4 1.0 ND1 B:HIS67 4.3 30.4 1.0 CG B:HIS67 4.5 31.7 1.0 CG B:GLU92 4.7 37.1 1.0 CA B:CYS65 4.9 30.6 1.0

J.Wielens, S.J.Headey, D.I.Rhodes, R.J.Mulder, O.Dolezal, J.J.Deadman, J.Newman, D.K.Chalmers, M.W.Parker, T.S.Peat, M.J.Scanlon. Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification? J Biomol Screen V. 18 147 2013.
ISSN: ISSN 1087-0571
PubMed: 23139382
DOI: 10.1177/1087057112465979