Cadmium in PDB 3wnf: Cyclic Hexapeptide Ckidnc in Complex with Hiv-1 Integrase

The structure of Cyclic Hexapeptide Ckidnc in Complex with Hiv-1 Integrase, PDB code: 3wnf 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)	43.36 / 1.45
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	50.070, 50.070, 102.570, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.2

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

Cadmium binding site 1 out of 4 in the Cyclic Hexapeptide Ckidnc 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 Ckidnc in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:15.0 occ:1.00 O A:HOH1111 2.3 13.4 1.0 CL A:CL1003 2.5 15.8 1.0 OD2 A:ASP116 2.5 14.8 1.0 OE2 A:GLU92 2.5 14.7 1.0 SG A:CYS65 2.6 14.4 1.0 CG A:ASP116 3.4 14.0 1.0 CD A:GLU92 3.5 12.7 1.0 OD1 A:ASP116 3.6 13.8 1.0 CB A:CYS65 3.6 9.4 1.0 CD A:CD1002 3.7 15.7 1.0 O A:HOH1139 4.0 17.1 1.0 O A:HOH1128 4.1 20.1 1.0 OD1 A:ASN120 4.2 15.2 1.0 OE1 A:GLU92 4.2 18.0 1.0 O A:HOH1114 4.4 18.5 1.0 O A:HOH1109 4.4 17.4 1.0 CG A:GLU92 4.5 12.3 1.0 N A:CYS65 4.6 15.9 1.0 ND2 A:ASN120 4.7 14.5 1.0 CA A:CYS65 4.7 14.1 1.0 CB A:ASP116 4.7 16.8 1.0 CG A:ASN120 4.9 16.1 1.0

Cadmium binding site 2 out of 4 in the Cyclic Hexapeptide Ckidnc 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 Ckidnc in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:15.7 occ:1.00 NE2 A:HIS67 2.3 14.1 1.0 OE1 A:GLU92 2.4 18.0 1.0 SG A:CYS65 2.6 14.4 1.0 OE2 A:GLU92 2.9 14.7 1.0 CD A:GLU92 3.1 12.7 1.0 CE1 A:HIS67 3.1 18.8 1.0 CD2 A:HIS67 3.3 16.1 1.0 CB A:CYS65 3.5 9.4 1.0 CD A:CD1001 3.7 15.0 1.0 ND1 A:HIS67 4.3 20.4 1.0 CG A:HIS67 4.4 15.2 1.0 CG A:GLU92 4.5 12.3 1.0 O A:HOH1133 4.6 29.2 1.0 C A:CYS65 4.7 12.1 1.0 CA A:CYS65 4.7 14.1 1.0

Cadmium binding site 3 out of 4 in the Cyclic Hexapeptide Ckidnc 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 Ckidnc in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:15.6 occ:1.00 NE2 B:HIS67 2.2 15.4 1.0 OE1 B:GLU92 2.4 18.7 1.0 SG B:CYS65 2.6 15.2 1.0 OE2 B:GLU92 3.0 15.5 1.0 CD B:GLU92 3.0 13.4 1.0 CE1 B:HIS67 3.1 18.8 1.0 CD2 B:HIS67 3.3 16.9 1.0 CB B:CYS65 3.5 9.9 1.0 CD B:CD302 3.7 14.8 1.0 ND1 B:HIS67 4.3 21.1 1.0 CG B:HIS67 4.4 14.7 1.0 CG B:GLU92 4.5 12.2 1.0 O B:HOH447 4.7 26.7 1.0 C B:CYS65 4.7 13.7 1.0 CA B:CYS65 4.7 14.2 1.0

Cadmium binding site 4 out of 4 in the Cyclic Hexapeptide Ckidnc 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 Ckidnc in Complex with Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:14.8 occ:1.00 O B:HOH410 2.3 11.9 1.0 CL B:CL303 2.5 15.8 1.0 OD2 B:ASP116 2.5 14.8 1.0 OE2 B:GLU92 2.5 15.5 1.0 SG B:CYS65 2.6 15.2 1.0 CG B:ASP116 3.4 15.0 1.0 CD B:GLU92 3.5 13.4 1.0 OD1 B:ASP116 3.6 13.6 1.0 CB B:CYS65 3.6 9.9 1.0 CD B:CD301 3.7 15.6 1.0 O B:HOH414 4.0 16.9 1.0 O B:HOH430 4.1 21.1 1.0 OE1 B:GLU92 4.1 18.7 1.0 ND2 B:ASN120 4.2 12.8 1.0 O B:HOH417 4.4 16.8 1.0 CG B:GLU92 4.5 12.2 1.0 N B:CYS65 4.6 16.2 1.0 OD1 B:ASN120 4.7 17.1 1.0 CB B:ASP116 4.7 16.9 1.0 CA B:CYS65 4.7 14.2 1.0 CG B:ASN120 4.9 18.1 1.0 CE2 B:PHE121 5.0 19.1 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.