Cadmium in PDB 4y1c: 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: 4y1c 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)	28.35 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.480, 61.500, 81.440, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 29.5

The binding sites of Cadmium atom in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain (pdb code 4y1c). 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: 4y1c:
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:Cd301 b:24.7 occ:1.00 OE1 A:GLU92 1.9 17.9 1.0 NE2 A:HIS67 2.3 17.6 1.0 SG A:CYS65 2.6 19.8 1.0 CD A:GLU92 3.0 24.1 1.0 CD2 A:HIS67 3.2 17.0 1.0 CE1 A:HIS67 3.3 18.4 1.0 CB A:CYS65 3.4 19.9 1.0 CD A:CD302 3.5 26.9 1.0 OE2 A:GLU92 3.6 23.5 1.0 CG A:GLU92 4.2 25.1 1.0 CG A:HIS67 4.4 20.6 1.0 ND1 A:HIS67 4.4 19.3 1.0 CA A:CYS65 4.7 23.1 1.0 C A:CYS65 4.9 20.9 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:Cd302 b:26.9 occ:1.00 OD2 A:ASP116 2.3 17.8 1.0 OE2 A:GLU92 2.4 23.5 1.0 SG A:CYS65 2.6 19.8 1.0 CG A:ASP116 3.2 18.1 1.0 CD A:GLU92 3.2 24.1 1.0 CB A:CYS65 3.2 19.9 1.0 OD1 A:ASP116 3.3 18.8 1.0 OE1 A:GLU92 3.4 17.9 1.0 CD A:CD301 3.5 24.7 1.0 N A:CYS65 4.3 27.3 1.0 CA A:CYS65 4.4 23.1 1.0 OD1 A:ASN120 4.5 17.0 1.0 CG A:GLU92 4.6 25.1 1.0 CB A:ASP116 4.7 19.1 1.0 CE2 A:PHE121 4.7 21.4 1.0 ND2 A:ASN120 4.8 16.2 1.0 CA A:GLY118 5.0 16.7 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:Cd1001 b:39.5 occ:1.00 OE2 B:GLU92 2.0 31.6 1.0 OD2 B:ASP116 2.0 25.4 1.0 CB B:CYS65 2.9 28.8 1.0 CD B:GLU92 3.1 33.5 1.0 SG B:CYS65 3.1 41.9 1.0 CG B:ASP116 3.2 32.1 1.0 CD B:CD1002 3.4 53.6 0.9 OE1 B:GLU92 3.6 26.6 1.0 OD1 B:ASP116 3.7 32.1 1.0 CA B:CYS65 4.1 31.8 1.0 OD1 B:ASN120 4.2 31.2 1.0 N B:CYS65 4.2 32.4 1.0 CG B:GLU92 4.3 33.3 1.0 CE2 B:PHE121 4.3 32.0 1.0 ND2 B:ASN120 4.4 28.5 1.0 CB B:ASP116 4.5 31.9 1.0 CG B:ASN120 4.8 31.8 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:Cd1002 b:53.6 occ:0.90 OE1 B:GLU92 2.1 26.6 1.0 NE2 B:HIS67 2.3 48.5 1.0 SG B:CYS65 3.0 41.9 1.0 CD B:GLU92 3.0 33.5 1.0 CE1 B:HIS67 3.1 45.5 1.0 CB B:CYS65 3.2 28.8 1.0 OE2 B:GLU92 3.3 31.6 1.0 CD2 B:HIS67 3.4 47.3 1.0 CD B:CD1001 3.4 39.5 1.0 ND1 B:HIS67 4.3 44.0 1.0 CG B:GLU92 4.4 33.3 1.0 CG B:HIS67 4.5 45.9 1.0 CA B:CYS65 4.7 31.8 1.0 OD2 B:ASP116 4.9 25.4 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.