Cadmium in PDB 3vqp: Hiv-1 in Core Domain in Complex with 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol

The structure of Hiv-1 in Core Domain in Complex with 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol, PDB code: 3vqp 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)	41.06 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.850, 63.180, 82.130, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.6

The structure of Hiv-1 in Core Domain in Complex with 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol (pdb code 3vqp). 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 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol, PDB code: 3vqp:
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 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol


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 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:37.3 occ:0.86 OE1 A:GLU92 2.2 27.5 1.0 NE2 A:HIS67 2.3 38.9 1.0 SG A:CYS65 2.5 33.7 1.0 O A:HOH410 2.6 46.2 1.0 CD A:GLU92 3.0 39.3 1.0 CD2 A:HIS67 3.2 35.0 1.0 OE2 A:GLU92 3.2 29.6 1.0 CB A:CYS65 3.3 36.1 1.0 CE1 A:HIS67 3.4 34.7 1.0 CD A:CD302 3.5 38.4 1.0 O A:HOH408 3.9 55.8 1.0 O A:HOH411 4.3 41.7 1.0 CG A:HIS67 4.4 33.6 1.0 CG A:GLU92 4.4 38.9 1.0 ND1 A:HIS67 4.5 35.1 1.0 O A:HOH403 4.6 36.7 1.0 CA A:CYS65 4.7 39.1 1.0 O A:HOH412 4.9 52.0 1.0 C A:CYS65 5.0 35.8 1.0

Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol


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 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:38.4 occ:1.00 OD1 A:ASP116 2.2 41.6 1.0 O A:HOH402 2.4 33.1 1.0 OE2 A:GLU92 2.5 29.6 1.0 CL A:CL303 2.6 49.1 1.0 SG A:CYS65 2.8 33.7 1.0 CG A:ASP116 3.1 32.8 1.0 CB A:CYS65 3.3 36.1 1.0 OD2 A:ASP116 3.3 38.9 1.0 CD A:CD301 3.5 37.3 0.9 CD A:GLU92 3.6 39.3 1.0 O A:HOH409 3.8 40.6 1.0 O A:HOH412 4.0 52.0 1.0 OE1 A:GLU92 4.0 27.5 1.0 O A:HOH403 4.2 36.7 1.0 N A:CYS65 4.3 38.1 1.0 CA A:CYS65 4.4 39.1 1.0 O A:HOH401 4.4 37.5 1.0 CB A:ASP116 4.5 35.8 1.0 CE2 A:PHE121 4.6 45.9 1.0 OD1 A:ASN120 4.7 36.5 1.0 CG A:GLU92 4.8 38.9 1.0 O A:HOH410 4.8 46.2 1.0 O A:HOH408 4.9 55.8 1.0

Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol


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 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:48.1 occ:1.00 OE2 B:GLU92 2.3 40.8 1.0 O B:HOH414 2.5 46.5 1.0 SG B:CYS65 2.6 43.0 1.0 O B:HOH402 2.7 31.7 1.0 OD1 B:ASP116 2.8 33.2 1.0 O B:HOH413 2.9 61.4 1.0 CD B:GLU92 3.4 54.8 1.0 CB B:CYS65 3.4 38.9 1.0 CD B:CD302 3.5 57.0 1.0 OD2 B:ASP116 3.5 42.1 1.0 CG B:ASP116 3.5 39.4 1.0 OE1 B:GLU92 3.7 31.2 1.0 O B:HOH410 3.9 56.7 1.0 N B:CYS65 4.5 37.9 1.0 O B:HOH407 4.5 44.1 1.0 O B:HOH412 4.6 60.5 1.0 CE2 B:PHE121 4.6 39.9 1.0 O B:HOH409 4.6 61.3 1.0 CA B:CYS65 4.6 36.3 1.0 CG B:GLU92 4.7 45.0 1.0 ND2 B:ASN120 4.8 46.1 1.0 OD1 B:ASN120 4.8 59.4 1.0 CB B:ASP116 5.0 37.9 1.0

Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol


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 2,3-Dihydro-1,4-Benzodioxin-5- Ylmethanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:57.0 occ:1.00 OE1 B:GLU92 2.2 31.2 1.0 NE2 B:HIS67 2.2 47.1 1.0 O B:HOH413 2.6 61.4 1.0 SG B:CYS65 2.6 43.0 1.0 O B:HOH406 2.8 30.9 1.0 O B:HOH411 3.0 49.3 1.0 CD2 B:HIS67 3.1 47.9 1.0 CD B:GLU92 3.1 54.8 1.0 CE1 B:HIS67 3.2 58.0 1.0 OE2 B:GLU92 3.4 40.8 1.0 CD B:CD301 3.5 48.1 1.0 CB B:CYS65 3.6 38.9 1.0 O B:HOH409 4.3 61.3 1.0 CG B:HIS67 4.3 50.8 1.0 ND1 B:HIS67 4.3 49.7 1.0 O B:HOH412 4.3 60.5 1.0 CG B:GLU92 4.5 45.0 1.0 CA B:CYS65 4.9 36.3 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