Cadmium in PDB 3wng: Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase

The structure of Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase, PDB code: 3wng 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)	40.07 / 1.75
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	50.250, 50.250, 102.710, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 22.2

The structure of Cyclic Hexapeptide Pkidnp 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 Pkidnp in Complex with Hiv-1 Integrase (pdb code 3wng). 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 Pkidnp in Complex with Hiv-1 Integrase, PDB code: 3wng:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Cyclic Hexapeptide Pkidnp 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 Pkidnp in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:18.2 occ:1.00 OE1 A:GLU92 2.1 20.7 1.0 NE2 A:HIS67 2.1 17.9 1.0 SG A:CYS65 2.5 16.8 1.0 CD A:GLU92 2.9 17.9 1.0 OE2 A:GLU92 3.0 17.5 1.0 CE1 A:HIS67 3.0 19.7 1.0 CD2 A:HIS67 3.2 19.7 1.0 CB A:CYS65 3.5 17.2 1.0 CD A:CD1002 3.8 17.2 1.0 ND1 A:HIS67 4.2 22.6 1.0 CG A:HIS67 4.3 17.9 1.0 CG A:GLU92 4.4 16.7 1.0 CA A:CYS65 4.7 15.7 1.0 C A:CYS65 4.7 14.4 1.0 O A:HOH1163 4.7 34.0 1.0 O2 A:SO41005 4.9 72.6 1.0 N A:THR66 4.9 15.3 1.0

Cadmium binding site 2 out of 4 in the Cyclic Hexapeptide Pkidnp 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 Pkidnp in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:17.2 occ:1.00 O A:HOH1101 2.4 15.0 1.0 OD2 A:ASP116 2.4 18.6 1.0 OE2 A:GLU92 2.5 17.5 1.0 CL A:CL1003 2.5 16.1 1.0 SG A:CYS65 2.5 16.8 1.0 CD A:GLU92 3.3 17.9 1.0 CG A:ASP116 3.4 15.8 1.0 CB A:CYS65 3.6 17.2 1.0 OD1 A:ASP116 3.6 18.4 1.0 CD A:CD1001 3.8 18.2 1.0 OE1 A:GLU92 3.9 20.7 1.0 O A:HOH1115 3.9 19.1 1.0 O A:HOH1109 4.0 17.9 1.0 OD1 A:ASN120 4.2 20.8 1.0 CG A:GLU92 4.4 16.7 1.0 O A:HOH1102 4.4 17.0 1.0 N A:CYS65 4.5 18.1 1.0 CA A:CYS65 4.6 15.7 1.0 ND2 A:ASN120 4.7 14.9 1.0 CB A:ASP116 4.8 17.2 1.0 CG A:ASN120 4.9 16.6 1.0

Cadmium binding site 3 out of 4 in the Cyclic Hexapeptide Pkidnp 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 Pkidnp in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:18.0 occ:1.00 OE1 B:GLU92 1.9 21.5 1.0 NE2 B:HIS67 2.2 17.0 1.0 SG B:CYS65 2.5 16.8 1.0 CD B:GLU92 2.9 17.1 1.0 OE2 B:GLU92 3.0 17.7 1.0 CE1 B:HIS67 3.1 19.8 1.0 CD2 B:HIS67 3.2 19.2 1.0 CB B:CYS65 3.4 17.7 1.0 CD B:CD302 3.8 17.3 1.0 ND1 B:HIS67 4.3 22.6 1.0 CG B:HIS67 4.3 17.9 1.0 CG B:GLU92 4.4 16.7 1.0 O B:HOH434 4.5 38.1 1.0 CA B:CYS65 4.7 15.9 1.0 C B:CYS65 4.7 14.7 1.0 N B:THR66 5.0 15.4 1.0

Cadmium binding site 4 out of 4 in the Cyclic Hexapeptide Pkidnp 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 Pkidnp in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:17.3 occ:1.00 O B:HOH401 2.4 15.7 1.0 OD2 B:ASP116 2.4 18.9 1.0 OE2 B:GLU92 2.4 17.7 1.0 CL B:CL303 2.5 16.7 1.0 SG B:CYS65 2.6 16.8 1.0 CD B:GLU92 3.4 17.1 1.0 CG B:ASP116 3.4 15.7 1.0 OD1 B:ASP116 3.6 19.2 1.0 CB B:CYS65 3.6 17.7 1.0 CD B:CD301 3.8 18.0 1.0 OE1 B:GLU92 3.9 21.5 1.0 O B:HOH413 3.9 19.8 1.0 O B:HOH405 4.1 20.1 1.0 OD1 B:ASN120 4.2 19.7 1.0 CG B:GLU92 4.4 16.7 1.0 O B:HOH402 4.4 16.4 1.0 N B:CYS65 4.5 17.2 1.0 CA B:CYS65 4.6 15.9 1.0 ND2 B:ASN120 4.7 15.7 1.0 CB B:ASP116 4.8 16.9 1.0 CG B:ASN120 4.9 17.2 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.