Cadmium in PDB 3vqa: Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide

The structure of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide, PDB code: 3vqa 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)	48.91 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.873, 61.023, 81.917, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.9

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide (pdb code 3vqa). 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 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide, PDB code: 3vqa:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:20.6 occ:0.80 OE1 A:GLU92 2.0 18.8 1.0 SG A:CYS65 2.5 28.2 1.0 NE2 A:HIS67 2.5 24.6 1.0 CD A:GLU92 3.1 35.4 1.0 CD2 A:HIS67 3.1 24.7 1.0 CB A:CYS65 3.5 20.4 1.0 CD A:CD302 3.5 29.8 1.0 OE2 A:GLU92 3.5 37.6 1.0 CE1 A:HIS67 3.6 23.2 1.0 CG A:GLU92 4.4 34.4 1.0 CG A:HIS67 4.4 23.9 1.0 ND1 A:HIS67 4.6 24.3 1.0 CA A:CYS65 4.8 21.2 1.0 C A:CYS65 4.9 21.5 1.0

Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:29.8 occ:1.00 O A:HOH428 2.2 28.4 1.0 OD2 A:ASP116 2.4 29.2 1.0 SG A:CYS65 2.7 28.2 1.0 OE2 A:GLU92 2.9 37.6 1.0 CG A:ASP116 3.3 23.9 1.0 OD1 A:ASP116 3.3 26.6 1.0 CB A:CYS65 3.4 20.4 1.0 CD A:CD301 3.5 20.6 0.8 CD A:GLU92 3.7 35.4 1.0 OE1 A:GLU92 3.8 18.8 1.0 N A:CYS65 4.5 22.1 1.0 CA A:CYS65 4.6 21.2 1.0 OD1 A:ASN120 4.6 26.8 1.0 OD1 A:ASP64 4.7 54.1 1.0 CB A:ASP116 4.7 23.0 1.0 O A:HOH429 4.8 24.0 1.0 CE2 A:PHE121 4.8 30.3 1.0

Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:36.8 occ:1.00 OD2 B:ASP116 2.2 25.0 1.0 OE2 B:GLU92 2.3 34.9 1.0 O B:HOH433 2.6 19.6 1.0 O B:HOH441 2.6 30.3 1.0 SG B:CYS65 2.7 34.6 1.0 O B:HOH426 2.7 30.3 1.0 CD B:GLU92 3.2 31.8 1.0 CG B:ASP116 3.2 30.5 1.0 CB B:CYS65 3.4 32.0 1.0 OE1 B:GLU92 3.4 23.1 1.0 CD B:CD302 3.5 39.4 1.0 OD1 B:ASP116 3.6 29.6 1.0 N B:CYS65 4.3 31.2 1.0 OD1 B:ASN120 4.4 36.7 1.0 O B:HOH435 4.4 32.0 1.0 CA B:CYS65 4.5 30.1 1.0 CG B:GLU92 4.6 28.2 1.0 CB B:ASP116 4.6 32.5 1.0 ND2 B:ASN120 4.8 32.6 1.0 CE2 B:PHE121 4.9 27.8 1.0 O B:HOH434 4.9 34.9 1.0

Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:39.4 occ:1.00 O B:HOH435 2.0 32.0 1.0 NE2 B:HIS67 2.3 36.9 1.0 OE1 B:GLU92 2.5 23.1 1.0 O B:HOH426 2.5 30.3 1.0 SG B:CYS65 2.6 34.6 1.0 O B:HOH434 2.7 34.9 1.0 CD2 B:HIS67 3.2 36.6 1.0 CE1 B:HIS67 3.2 41.1 1.0 CD B:CD301 3.5 36.8 1.0 CD B:GLU92 3.5 31.8 1.0 CB B:CYS65 3.6 32.0 1.0 OE2 B:GLU92 3.9 34.9 1.0 ND1 B:HIS67 4.4 38.5 1.0 CG B:HIS67 4.4 38.6 1.0 CG B:GLU92 4.8 28.2 1.0 CA B:CYS65 4.9 30.1 1.0 OD2 B:ASP116 5.0 25.0 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