Chlorine 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:

Cadmium

(Cd)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain, PDB code: 4y1d:
Jump to Chlorine binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1003 b:45.7 occ:1.00 CD A:CD1002 2.7 41.1 1.0 CE2 A:PHE121 3.1 39.9 1.0 OD2 A:ASP116 3.4 36.2 1.0 CZ A:PHE121 3.4 38.3 1.0 ND2 A:ASN120 3.7 30.9 1.0 OE2 A:GLU92 3.8 49.2 1.0 CB A:CYS65 3.8 38.6 1.0 CD2 A:LEU74 3.9 39.5 1.0 O A:HOH1107 3.9 35.1 1.0 N A:CYS65 4.0 37.1 1.0 CG A:ASP116 4.0 40.0 1.0 SG A:CYS65 4.0 35.9 1.0 OD1 A:ASP116 4.1 42.5 1.0 C A:ASP64 4.2 41.8 1.0 CD2 A:PHE121 4.4 32.6 1.0 CA A:CYS65 4.4 31.6 1.0 CA A:ASP64 4.4 39.5 1.0 OD1 A:ASN120 4.5 38.4 1.0 CD A:GLU92 4.5 43.8 1.0 CG A:ASN120 4.6 42.5 1.0 N A:ASP64 4.7 35.7 1.0 O A:LEU63 4.7 38.3 1.0 O A:ASP64 4.7 36.4 1.0 CE1 A:PHE121 4.8 38.5 1.0 CG A:GLU92 4.8 48.9 1.0 C A:LEU63 4.9 37.7 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 B:Cl303 b:46.6 occ:1.00 CD B:CD302 2.7 31.4 1.0 CE2 B:PHE121 3.2 30.5 1.0 O B:HOH404 3.4 35.0 1.0 OE2 B:GLU92 3.4 41.5 1.0 O B:HOH405 3.4 35.5 1.0 CB B:CYS65 3.6 31.6 1.0 OD2 B:ASP116 3.6 28.7 1.0 CZ B:PHE121 3.7 34.0 1.0 CD2 B:LEU74 3.8 40.3 1.0 ND2 B:ASN120 3.9 27.3 1.0 OD1 B:ASP116 3.9 30.5 1.0 N B:CYS65 4.0 27.1 1.0 SG B:CYS65 4.0 27.6 1.0 CG B:ASP116 4.1 30.8 1.0 CD B:GLU92 4.2 34.2 1.0 C B:ASP64 4.2 31.6 1.0 CA B:CYS65 4.3 23.4 1.0 CD2 B:PHE121 4.4 32.9 1.0 OD1 B:ASN120 4.4 32.2 1.0 CG B:GLU92 4.6 33.9 1.0 CA B:ASP64 4.6 33.5 1.0 CG B:ASN120 4.6 30.6 1.0 O B:ASP64 4.6 36.5 1.0 N B:ASP64 5.0 29.9 1.0 O B:LEU63 5.0 29.3 1.0 OE1 B:GLU92 5.0 28.7 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.