Cadmium in PDB 3vq4: Fragments Bound to Hiv-1 Integrase

The structure of Fragments Bound to Hiv-1 Integrase, PDB code: 3vq4 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)	49.63 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.601, 62.323, 82.087, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.1

The binding sites of Cadmium atom in the Fragments Bound to Hiv-1 Integrase (pdb code 3vq4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Fragments Bound to Hiv-1 Integrase, PDB code: 3vq4:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Fragments Bound to Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Fragments Bound to Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:24.7 occ:0.70 OE1 A:GLU92 1.6 20.6 1.0 NE2 A:HIS67 2.5 24.0 1.0 SG A:CYS65 2.5 25.6 1.0 CD A:GLU92 2.6 32.8 1.0 OE2 A:GLU92 2.9 38.8 1.0 CE1 A:HIS67 3.3 28.7 1.0 CB A:CYS65 3.5 28.7 1.0 CD A:CD302 3.5 32.8 1.0 CD2 A:HIS67 3.5 29.5 1.0 O A:HOH434 3.8 56.1 1.0 CG A:GLU92 4.1 32.6 1.0 ND1 A:HIS67 4.5 23.0 1.0 CG A:HIS67 4.6 27.5 1.0 CA A:CYS65 4.8 28.7 1.0 C A:CYS65 4.9 29.5 1.0 CG1 A:VAL72 5.0 27.1 1.0

Cadmium binding site 2 out of 4 in the Fragments Bound to Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Fragments Bound to Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:32.8 occ:1.00 OE2 A:GLU92 2.5 38.8 1.0 OD2 A:ASP116 2.5 34.1 1.0 SG A:CYS65 2.6 25.6 1.0 O A:HOH401 2.6 20.6 1.0 CG A:ASP116 3.3 24.6 1.0 OD1 A:ASP116 3.3 27.9 1.0 CB A:CYS65 3.4 28.7 1.0 CD A:CD301 3.5 24.7 0.7 CD A:GLU92 3.5 32.8 1.0 OE1 A:GLU92 3.9 20.6 1.0 N A:CYS65 4.3 30.1 1.0 CA A:CYS65 4.5 28.7 1.0 O A:HOH434 4.5 56.1 1.0 OD1 A:ASN120 4.6 25.2 1.0 O A:HOH408 4.7 31.9 1.0 CB A:ASP116 4.7 25.2 1.0 CG A:GLU92 4.8 32.6 1.0 CE2 A:PHE121 4.9 33.7 1.0

Cadmium binding site 3 out of 4 in the Fragments Bound to Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Fragments Bound to Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:43.6 occ:1.00 OE2 B:GLU92 2.1 39.1 1.0 OD2 B:ASP116 2.3 32.3 1.0 O B:HOH430 2.6 35.4 1.0 SG B:CYS65 2.7 36.1 1.0 O B:HOH407 2.8 23.5 1.0 CD B:GLU92 3.2 40.0 1.0 CG B:ASP116 3.3 40.4 1.0 CB B:CYS65 3.5 39.2 1.0 OD1 B:ASP116 3.5 40.9 1.0 CD B:CD302 3.6 52.2 1.0 OE1 B:GLU92 3.7 44.0 1.0 N B:CYS65 4.3 39.1 1.0 CE2 B:PHE121 4.4 35.5 1.0 CG B:GLU92 4.5 39.4 1.0 OD1 B:ASN120 4.5 37.9 1.0 CA B:CYS65 4.6 38.5 1.0 O B:HOH418 4.6 39.9 1.0 CB B:ASP116 4.6 37.9 1.0 ND2 B:ASN120 4.8 35.5 1.0 O B:HOH435 4.9 42.1 1.0

Cadmium binding site 4 out of 4 in the Fragments Bound to Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Fragments Bound to Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:52.2 occ:1.00 NE2 B:HIS67 2.3 45.9 1.0 OE1 B:GLU92 2.4 44.0 1.0 SG B:CYS65 2.7 36.1 1.0 O B:HOH443 2.7 39.2 1.0 CD2 B:HIS67 3.2 44.5 1.0 CD B:GLU92 3.3 40.0 1.0 CE1 B:HIS67 3.4 44.4 1.0 OE2 B:GLU92 3.5 39.1 1.0 CD B:CD301 3.6 43.6 1.0 CB B:CYS65 3.7 39.2 1.0 CG B:HIS67 4.4 44.8 1.0 ND1 B:HIS67 4.5 44.7 1.0 O B:HOH435 4.6 42.1 1.0 CG B:GLU92 4.8 39.4 1.0 CA B:CYS65 4.9 38.5 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