Cadmium in PDB 3vq7: Hiv-1 in Core Domain in Complex with 4-(1H-Pyrrol-1-Yl)Aniline

The structure of Hiv-1 in Core Domain in Complex with 4-(1H-Pyrrol-1-Yl)Aniline, PDB code: 3vq7 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)	34.15 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.284, 61.658, 82.017, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.7

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with 4-(1H-Pyrrol-1-Yl)Aniline (pdb code 3vq7). 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 4-(1H-Pyrrol-1-Yl)Aniline, PDB code: 3vq7:
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 4-(1H-Pyrrol-1-Yl)Aniline


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 4-(1H-Pyrrol-1-Yl)Aniline within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:20.4 occ:1.00 OE1 A:GLU92 1.8 17.5 1.0 O A:HOH1155 2.3 20.7 1.0 NE2 A:HIS67 2.3 19.0 1.0 SG A:CYS65 2.5 17.0 1.0 CD A:GLU92 3.0 24.0 1.0 CE1 A:HIS67 3.3 19.3 1.0 CD2 A:HIS67 3.3 21.3 1.0 OE2 A:GLU92 3.4 22.6 1.0 CB A:CYS65 3.6 20.6 1.0 CD A:CD1002 3.6 23.4 1.0 CG A:GLU92 4.3 24.4 1.0 O A:HOH1135 4.3 36.6 1.0 ND1 A:HIS67 4.4 18.7 1.0 CG A:HIS67 4.4 21.6 1.0 CA A:CYS65 4.9 20.3 1.0 C A:CYS65 5.0 21.6 1.0

Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with 4-(1H-Pyrrol-1-Yl)Aniline


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 4-(1H-Pyrrol-1-Yl)Aniline within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:23.4 occ:1.00 O A:HOH1117 2.2 21.6 1.0 OD2 A:ASP116 2.4 23.1 1.0 SG A:CYS65 2.5 17.0 1.0 OE2 A:GLU92 2.5 22.6 1.0 O A:HOH1101 2.6 14.8 1.0 CG A:ASP116 3.4 18.6 1.0 CD A:GLU92 3.5 24.0 1.0 CB A:CYS65 3.5 20.6 1.0 OD1 A:ASP116 3.5 20.0 1.0 CD A:CD1001 3.6 20.4 1.0 OE1 A:GLU92 3.7 17.5 1.0 N A:CYS65 4.3 20.9 1.0 OD1 A:ASP64 4.3 32.7 1.0 CA A:CYS65 4.5 20.3 1.0 OD1 A:ASN120 4.6 21.1 1.0 O A:HOH1110 4.7 20.2 1.0 O A:HOH1155 4.7 20.7 1.0 CE2 A:PHE121 4.8 23.0 1.0 CB A:ASP116 4.8 18.1 1.0 CG A:GLU92 4.8 24.4 1.0 ND2 A:ASN120 5.0 17.9 1.0

Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with 4-(1H-Pyrrol-1-Yl)Aniline


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 4-(1H-Pyrrol-1-Yl)Aniline within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:31.9 occ:1.00 O B:HOH459 2.2 39.7 1.0 NE2 B:HIS67 2.2 34.4 1.0 OE1 B:GLU92 2.2 30.8 1.0 O B:HOH445 2.5 30.4 1.0 O B:HOH440 2.5 35.6 1.0 SG B:CYS65 2.6 28.2 1.0 CE1 B:HIS67 3.0 35.4 1.0 CD B:GLU92 3.2 28.4 1.0 CD2 B:HIS67 3.4 34.6 1.0 CB B:CYS65 3.5 28.2 1.0 OE2 B:GLU92 3.5 30.9 1.0 CD B:CD302 3.5 31.0 1.0 O B:HOH443 4.2 37.0 1.0 ND1 B:HIS67 4.2 35.3 1.0 CG B:HIS67 4.4 35.2 1.0 CG B:GLU92 4.6 28.0 1.0 CA B:CYS65 4.8 28.1 1.0 CB B:GLU92 5.0 26.2 1.0

Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with 4-(1H-Pyrrol-1-Yl)Aniline


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 4-(1H-Pyrrol-1-Yl)Aniline within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:31.0 occ:1.00 OE2 B:GLU92 2.2 30.9 1.0 O B:HOH424 2.3 23.2 1.0 OD2 B:ASP116 2.4 27.5 1.0 SG B:CYS65 2.5 28.2 1.0 O B:HOH440 2.6 35.6 1.0 O B:HOH409 2.7 16.7 1.0 CD B:GLU92 3.2 28.4 1.0 CG B:ASP116 3.4 27.4 1.0 CB B:CYS65 3.4 28.2 1.0 CD B:CD301 3.5 31.9 1.0 OD1 B:ASP116 3.6 26.7 1.0 OE1 B:GLU92 3.6 30.8 1.0 N B:CYS65 4.3 27.9 1.0 OD1 B:ASN120 4.3 30.1 1.0 O B:HOH414 4.4 28.9 1.0 CG B:GLU92 4.5 28.0 1.0 CA B:CYS65 4.5 28.1 1.0 CE2 B:PHE121 4.5 32.6 1.0 O B:HOH459 4.6 39.7 1.0 OD1 B:ASP64 4.7 38.5 1.0 O B:HOH443 4.7 37.0 1.0 CB B:ASP116 4.8 28.4 1.0 ND2 B:ASN120 4.8 25.1 1.0 O B:HOH445 4.9 30.4 1.0 CG B:ASN120 5.0 30.3 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