Cadmium in PDB 3wnh: Cyclic Hexapeptide Pkzdnv in Complex with Hiv-1 Integrase

The structure of Cyclic Hexapeptide Pkzdnv in Complex with Hiv-1 Integrase, PDB code: 3wnh was solved by J.Wielens, D.K.Chalmers, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.82 / 1.50
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	49.440, 49.440, 101.330, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.7

The structure of Cyclic Hexapeptide Pkzdnv in Complex with Hiv-1 Integrase also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

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

Cadmium binding site 1 out of 4 in the Cyclic Hexapeptide Pkzdnv in Complex with 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 Cyclic Hexapeptide Pkzdnv in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:14.6 occ:1.00 NE2 A:HIS67 2.1 13.0 1.0 OE1 A:GLU92 2.3 19.4 1.0 SG A:CYS65 2.6 14.0 1.0 OE2 A:GLU92 2.9 14.2 1.0 CD A:GLU92 2.9 15.0 1.0 CE1 A:HIS67 3.0 16.4 1.0 CD2 A:HIS67 3.2 16.7 1.0 CB A:CYS65 3.4 10.2 1.0 CD A:CD1002 3.7 13.9 1.0 O A:HOH1104 3.7 12.0 1.0 ND1 A:HIS67 4.2 17.8 1.0 CG A:GLU92 4.3 13.1 1.0 CG A:HIS67 4.3 14.8 1.0 O A:HOH1131 4.5 26.5 1.0 CA A:CYS65 4.6 13.9 1.0 C A:CYS65 4.6 12.6 1.0 O2 A:SO41005 4.7 47.5 1.0 O A:HOH1155 4.9 42.0 1.0 O A:CYS65 4.9 15.4 1.0 CB A:GLU92 4.9 11.7 1.0

Cadmium binding site 2 out of 4 in the Cyclic Hexapeptide Pkzdnv in Complex with 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 Cyclic Hexapeptide Pkzdnv in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:13.9 occ:1.00 O A:HOH1107 2.3 11.0 1.0 O A:HOH1104 2.3 12.0 1.0 CL A:CL1003 2.5 14.7 1.0 OD2 A:ASP116 2.5 13.7 1.0 OE2 A:GLU92 2.5 14.2 1.0 SG A:CYS65 2.5 14.0 1.0 CG A:ASP116 3.4 11.9 1.0 CD A:GLU92 3.4 15.0 1.0 CB A:CYS65 3.6 10.2 1.0 OD1 A:ASP116 3.6 14.5 1.0 CD A:CD1001 3.7 14.6 1.0 OE1 A:GLU92 4.0 19.4 1.0 O A:HOH1122 4.1 19.1 1.0 OD1 A:ASN120 4.2 13.7 1.0 CG A:GLU92 4.3 13.1 1.0 O A:HOH1106 4.4 14.4 1.0 N A:CYS65 4.5 13.1 1.0 O A:HOH1110 4.5 18.3 1.0 CA A:CYS65 4.6 13.9 1.0 ND2 A:ASN120 4.6 12.3 1.0 CB A:ASP116 4.7 14.8 1.0 CG A:ASN120 4.9 12.1 1.0 CE2 A:PHE121 5.0 13.1 1.0

Cadmium binding site 3 out of 4 in the Cyclic Hexapeptide Pkzdnv in Complex with 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 Cyclic Hexapeptide Pkzdnv in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:14.7 occ:1.00 NE2 B:HIS67 2.2 12.9 1.0 OE1 B:GLU92 2.2 18.8 1.0 SG B:CYS65 2.6 14.2 1.0 OE2 B:GLU92 2.9 15.6 1.0 CD B:GLU92 2.9 15.0 1.0 CE1 B:HIS67 3.0 15.6 1.0 CD2 B:HIS67 3.2 15.9 1.0 CB B:CYS65 3.5 9.5 1.0 CD B:CD302 3.7 13.8 1.0 O B:HOH402 3.7 11.8 1.0 ND1 B:HIS67 4.2 17.9 1.0 CG B:HIS67 4.3 15.7 1.0 CG B:GLU92 4.4 12.3 1.0 O B:HOH521 4.4 26.1 1.0 O B:HOH447 4.5 28.2 1.0 CA B:CYS65 4.6 13.5 1.0 C B:CYS65 4.6 12.4 1.0 O B:HOH477 4.7 45.8 1.0 O B:CYS65 4.9 14.4 1.0 CB B:GLU92 4.9 11.8 1.0 O3 B:SO4305 5.0 45.1 1.0 N B:THR66 5.0 13.0 1.0

Cadmium binding site 4 out of 4 in the Cyclic Hexapeptide Pkzdnv in Complex with 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 Cyclic Hexapeptide Pkzdnv in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:13.8 occ:1.00 O B:HOH402 2.3 11.8 1.0 O B:HOH408 2.3 10.9 1.0 CL B:CL303 2.5 14.7 1.0 OE2 B:GLU92 2.5 15.6 1.0 OD2 B:ASP116 2.5 14.0 1.0 SG B:CYS65 2.5 14.2 1.0 CD B:GLU92 3.4 15.0 1.0 CG B:ASP116 3.4 12.5 1.0 CB B:CYS65 3.6 9.5 1.0 OD1 B:ASP116 3.6 15.3 1.0 CD B:CD301 3.7 14.7 1.0 OE1 B:GLU92 3.9 18.8 1.0 O B:HOH411 4.0 17.5 1.0 OD1 B:ASN120 4.2 13.9 1.0 O B:HOH409 4.3 13.7 1.0 CG B:GLU92 4.4 12.3 1.0 O B:HOH416 4.4 19.7 1.0 N B:CYS65 4.4 13.8 1.0 CA B:CYS65 4.6 13.5 1.0 ND2 B:ASN120 4.6 11.6 1.0 CB B:ASP116 4.7 15.0 1.0 CG B:ASN120 4.9 12.2 1.0 CE2 B:PHE121 5.0 11.9 1.0

S.E.Northfield, J.Wielens, S.J.Headey, M.Mulcair, M.J.Scanlon, M.W.Parker, P.E.Thompson, D.K.Chalmers. Hexapeptide Mimetics of Ledgf in Complex with Hiv-1 Integrase To Be Published.