Cadmium in PDB 4y1d: Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain

The structure of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain, PDB code: 4y1d was solved by J.Wielens, D.K.Chalmers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.50 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.800, 62.600, 82.000, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.1

The structure of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cadmium atom in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain (pdb code 4y1d). 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 Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain, PDB code: 4y1d:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:49.0 occ:1.00 OE1 A:GLU92 2.0 34.0 1.0 NE2 A:HIS67 2.2 41.9 1.0 SG A:CYS65 2.6 35.9 1.0 CD A:GLU92 2.9 43.8 1.0 OE2 A:GLU92 3.1 49.2 1.0 CE1 A:HIS67 3.2 45.6 1.0 CD2 A:HIS67 3.2 45.3 1.0 CD A:CD1002 3.4 41.1 1.0 CB A:CYS65 3.5 38.6 1.0 O4 A:SO41005 4.3 0.1 1.0 CG A:GLU92 4.3 48.9 1.0 ND1 A:HIS67 4.4 43.2 1.0 CG A:HIS67 4.4 43.8 1.0 CA A:CYS65 4.8 31.6 1.0 OD2 A:ASP116 4.9 36.2 1.0

Cadmium binding site 2 out of 4 in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:41.1 occ:1.00 OD2 A:ASP116 2.1 36.2 1.0 OE2 A:GLU92 2.2 49.2 1.0 SG A:CYS65 2.5 35.9 1.0 O A:HOH1107 2.6 35.1 1.0 CL A:CL1003 2.7 45.7 1.0 CG A:ASP116 3.2 40.0 1.0 CD A:GLU92 3.2 43.8 1.0 CB A:CYS65 3.4 38.6 1.0 CD A:CD1001 3.4 49.0 1.0 OD1 A:ASP116 3.6 42.5 1.0 OE1 A:GLU92 3.7 34.0 1.0 CG A:GLU92 4.2 48.9 1.0 N A:CYS65 4.4 37.1 1.0 OD1 A:ASN120 4.5 38.4 1.0 CB A:ASP116 4.5 37.5 1.0 CA A:CYS65 4.5 31.6 1.0 CE2 A:PHE121 4.7 39.9 1.0 ND2 A:ASN120 4.7 30.9 1.0 CG A:ASN120 5.0 42.5 1.0

Cadmium binding site 3 out of 4 in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:29.0 occ:1.00 OE1 B:GLU92 2.1 28.7 1.0 NE2 B:HIS67 2.3 22.5 1.0 SG B:CYS65 2.5 27.6 1.0 CD B:GLU92 3.1 34.2 1.0 CD2 B:HIS67 3.2 26.8 1.0 CE1 B:HIS67 3.3 24.6 1.0 OE2 B:GLU92 3.4 41.5 1.0 CD B:CD302 3.5 31.4 1.0 CB B:CYS65 3.6 31.6 1.0 ND1 B:HIS67 4.4 26.9 1.0 CG B:HIS67 4.5 26.3 1.0 CG B:GLU92 4.6 33.9 1.0 CA B:CYS65 4.9 23.4 1.0 C B:CYS65 4.9 27.6 1.0 O B:HOH427 5.0 29.6 1.0 O2 B:SO4305 5.0 0.1 1.0

Cadmium binding site 4 out of 4 in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:31.4 occ:1.00 OE2 B:GLU92 2.2 41.5 1.0 O B:HOH405 2.4 35.5 1.0 OD2 B:ASP116 2.4 28.7 1.0 SG B:CYS65 2.6 27.6 1.0 CL B:CL303 2.7 46.6 1.0 CD B:GLU92 3.2 34.2 1.0 CG B:ASP116 3.3 30.8 1.0 CB B:CYS65 3.5 31.6 1.0 OD1 B:ASP116 3.5 30.5 1.0 CD B:CD301 3.5 29.0 1.0 OE1 B:GLU92 3.6 28.7 1.0 O B:HOH427 4.2 29.6 1.0 CG B:GLU92 4.4 33.9 1.0 N B:CYS65 4.5 27.1 1.0 OD1 B:ASN120 4.5 32.2 1.0 CA B:CYS65 4.6 23.4 1.0 O B:HOH404 4.7 35.0 1.0 CB B:ASP116 4.8 28.7 1.0 CE2 B:PHE121 4.9 30.5 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.