Cadmium in PDB 3vqc: Hiv-1 in Core Domain in Complex with (5-Methyl-3-Phenyl-1,2-Oxazol-4- Yl)Methanol

The structure of Hiv-1 in Core Domain in Complex with (5-Methyl-3-Phenyl-1,2-Oxazol-4- Yl)Methanol, PDB code: 3vqc 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)	42.44 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.110, 59.920, 81.590, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.6

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with (5-Methyl-3-Phenyl-1,2-Oxazol-4- Yl)Methanol (pdb code 3vqc). 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-Oxazol-4- Yl)Methanol, PDB code: 3vqc:
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-Oxazol-4- Yl)Methanol


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-Oxazol-4- Yl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:40.9 occ:1.00 O A:HOH404 2.1 25.8 1.0 OE2 A:GLU92 2.2 29.5 1.0 NE2 A:HIS67 2.3 38.7 1.0 SG A:CYS65 2.4 41.1 1.0 CD A:GLU92 3.1 41.4 1.0 CD2 A:HIS67 3.2 37.9 1.0 CE1 A:HIS67 3.3 35.1 1.0 OE1 A:GLU92 3.4 46.5 1.0 CB A:CYS65 3.5 32.2 1.0 CD A:CD302 3.5 45.4 1.0 O A:HOH407 4.4 42.6 1.0 CG A:HIS67 4.5 45.6 1.0 ND1 A:HIS67 4.5 42.7 1.0 CG A:GLU92 4.5 41.8 1.0 CA A:CYS65 4.8 36.7 1.0 C A:CYS65 4.8 38.0 1.0 CG1 A:VAL72 4.9 37.9 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-Oxazol-4- Yl)Methanol


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-Oxazol-4- Yl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:45.4 occ:1.00 OD2 A:ASP116 2.5 40.6 1.0 OE1 A:GLU92 2.6 46.5 1.0 O A:HOH405 2.6 33.6 1.0 SG A:CYS65 2.6 41.1 1.0 CG A:ASP116 3.3 37.0 1.0 CB A:CYS65 3.4 32.2 1.0 OD1 A:ASP116 3.4 39.0 1.0 CD A:CD301 3.5 40.9 1.0 CD A:GLU92 3.6 41.4 1.0 O A:HOH407 3.9 42.6 1.0 OE2 A:GLU92 3.9 29.5 1.0 N A:CYS65 4.4 35.9 1.0 O A:HOH404 4.4 25.8 1.0 CA A:CYS65 4.5 36.7 1.0 O A:HOH406 4.6 54.4 1.0 OD1 A:ASN120 4.8 38.4 1.0 OD1 A:ASP64 4.8 49.3 0.6 CB A:ASP116 4.8 34.6 1.0 CE2 A:PHE121 4.8 41.1 1.0 CG A:GLU92 4.9 41.8 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-Oxazol-4- Yl)Methanol


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-Oxazol-4- Yl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:55.7 occ:1.00 OD2 B:ASP116 2.2 50.3 1.0 OE2 B:GLU92 2.4 40.4 1.0 O B:HOH405 2.6 35.0 1.0 O B:HOH404 2.7 37.2 1.0 SG B:CYS65 2.8 52.0 1.0 CB B:CYS65 3.1 39.7 1.0 CG B:ASP116 3.2 52.6 1.0 CD B:GLU92 3.4 36.1 1.0 CD B:CD302 3.5 59.4 1.0 OD1 B:ASP116 3.5 51.2 1.0 OE1 B:GLU92 4.2 33.8 1.0 N B:CYS65 4.2 41.0 1.0 CA B:CYS65 4.3 43.8 1.0 CG B:GLU92 4.3 39.9 1.0 OD1 B:ASN120 4.5 48.6 1.0 CB B:ASP116 4.6 54.0 1.0 O B:HOH406 4.6 43.5 1.0 OD1 B:ASP64 4.6 68.2 1.0 CE2 B:PHE121 4.8 54.5 1.0 ND2 B:ASN120 4.8 48.2 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-Oxazol-4- Yl)Methanol


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-Oxazol-4- Yl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:59.4 occ:1.00 OE1 B:GLU92 2.2 33.8 1.0 NE2 B:HIS67 2.3 51.8 1.0 OE2 B:GLU92 2.4 40.4 1.0 O B:HOH406 2.4 43.5 1.0 O B:HOH404 2.5 37.2 1.0 SG B:CYS65 2.6 52.0 1.0 CD B:GLU92 2.7 36.1 1.0 CE1 B:HIS67 3.3 56.0 1.0 CD2 B:HIS67 3.3 53.2 1.0 CB B:CYS65 3.4 39.7 1.0 CD B:CD301 3.5 55.7 1.0 O B:HOH410 3.7 59.1 1.0 CG B:GLU92 4.2 39.9 1.0 ND1 B:HIS67 4.4 56.1 1.0 CG B:HIS67 4.5 53.0 1.0 CA B:CYS65 4.8 43.8 1.0 CB B:GLU92 5.0 42.5 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