Cadmium in PDB 3vqd: Hiv-1 in Core Domain in Complex with 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid

The structure of Hiv-1 in Core Domain in Complex with 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid, PDB code: 3vqd 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)	40.96 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.857, 60.343, 81.922, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.1

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid (pdb code 3vqd). 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 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid, PDB code: 3vqd:
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 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid


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 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:24.1 occ:0.80 OE2 A:GLU92 2.0 17.0 1.0 O A:HOH416 2.4 24.6 1.0 NE2 A:HIS67 2.4 23.2 1.0 SG A:CYS65 2.5 23.7 1.0 CD A:GLU92 3.0 34.7 1.0 CD2 A:HIS67 3.1 22.6 1.0 OE1 A:GLU92 3.3 45.4 1.0 CB A:CYS65 3.5 26.0 1.0 CD A:CD302 3.6 32.5 1.0 CE1 A:HIS67 3.6 24.9 1.0 CG A:GLU92 4.3 34.1 1.0 CG A:HIS67 4.4 24.8 1.0 O A:HOH431 4.4 34.7 1.0 ND1 A:HIS67 4.6 24.4 1.0 CA A:CYS65 4.8 27.9 1.0 C A:CYS65 4.9 27.4 1.0

Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid


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 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:32.5 occ:1.00 O A:HOH430 2.2 36.6 1.0 OD2 A:ASP116 2.3 32.1 1.0 SG A:CYS65 2.6 23.7 1.0 O A:HOH403 2.7 19.4 1.0 OE1 A:GLU92 2.9 45.4 1.0 CG A:ASP116 3.2 25.6 1.0 OD1 A:ASP116 3.4 25.6 1.0 CB A:CYS65 3.4 26.0 1.0 CD A:CD301 3.6 24.1 0.8 CD A:GLU92 3.8 34.7 1.0 OE2 A:GLU92 4.1 17.0 1.0 N A:CYS65 4.4 28.4 1.0 CA A:CYS65 4.5 27.9 1.0 O A:HOH402 4.7 28.6 1.0 CB A:ASP116 4.7 23.9 1.0 OD1 A:ASP64 4.7 55.5 1.0 OD1 A:ASN120 4.7 26.3 1.0 CE2 A:PHE121 4.7 26.5 1.0 O A:HOH416 4.8 24.6 1.0

Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid


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 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:36.5 occ:1.00 OE2 B:GLU92 2.1 37.8 1.0 OD2 B:ASP116 2.2 30.2 1.0 O B:HOH427 2.4 42.1 1.0 O B:HOH428 2.5 34.6 1.0 SG B:CYS65 2.7 36.1 1.0 O B:HOH402 2.7 21.2 1.0 CD B:GLU92 3.0 35.2 1.0 CG B:ASP116 3.2 35.6 1.0 OE1 B:GLU92 3.3 26.7 1.0 CB B:CYS65 3.4 28.4 1.0 CD B:CD302 3.5 41.6 0.9 OD1 B:ASP116 3.5 33.8 1.0 N B:CYS65 4.3 26.9 1.0 CG B:GLU92 4.4 37.5 1.0 CA B:CYS65 4.5 28.4 1.0 O B:HOH434 4.5 30.0 1.0 O B:HOH413 4.6 34.4 1.0 CB B:ASP116 4.6 32.4 1.0 OD1 B:ASN120 4.6 41.0 1.0 CE2 B:PHE121 4.6 28.7 1.0 ND2 B:ASN120 4.8 37.1 1.0

Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid


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 5-Methyl-3-Phenyl-1,2-Oxazole-4- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:41.6 occ:0.90 O B:HOH434 2.2 30.0 1.0 O B:HOH427 2.2 42.1 1.0 OE1 B:GLU92 2.4 26.7 1.0 SG B:CYS65 2.5 36.1 1.0 O B:HOH426 2.7 34.5 1.0 NE2 B:HIS67 2.8 41.2 1.0 CE1 B:HIS67 3.1 44.7 1.0 CD B:GLU92 3.5 35.2 1.0 CD B:CD301 3.5 36.5 1.0 CB B:CYS65 3.5 28.4 1.0 OE2 B:GLU92 3.8 37.8 1.0 CD2 B:HIS67 3.9 46.8 1.0 ND1 B:HIS67 4.2 41.6 1.0 CG B:HIS67 4.7 45.7 1.0 CG B:GLU92 4.8 37.5 1.0 CA B:CYS65 4.9 28.4 1.0 OD2 B:ASP116 5.0 30.2 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