Zinc in PDB 4wnt: Human Cytochrome P450 2D6 Ajmalicine Complex

All present enzymatic activity of Human Cytochrome P450 2D6 Ajmalicine Complex:
1.14.14.1;

The structure of Human Cytochrome P450 2D6 Ajmalicine Complex, PDB code: 4wnt was solved by A.Wang, C.D.Stout, E.F.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.67 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.310, 126.810, 191.730, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.7

The structure of Human Cytochrome P450 2D6 Ajmalicine Complex also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Human Cytochrome P450 2D6 Ajmalicine Complex (pdb code 4wnt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human Cytochrome P450 2D6 Ajmalicine Complex, PDB code: 4wnt:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human Cytochrome P450 2D6 Ajmalicine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Cytochrome P450 2D6 Ajmalicine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:48.5 occ:1.00 NE2 A:HIS258 2.1 34.2 1.0 OE1 A:GLU273 2.2 42.1 1.0 OD2 A:ASP270 2.3 38.9 1.0 CD A:GLU273 3.0 42.4 1.0 CE1 A:HIS258 3.1 41.0 1.0 CD2 A:HIS258 3.1 42.8 1.0 CG A:ASP270 3.2 37.2 1.0 CG A:GLU273 3.2 41.5 1.0 OD1 A:ASP270 3.4 36.3 1.0 CG A:ARG269 4.0 44.4 1.0 NH1 A:ARG269 4.1 44.6 1.0 OE2 A:GLU273 4.2 45.0 1.0 ND1 A:HIS258 4.2 42.2 1.0 CG A:HIS258 4.2 42.3 1.0 CA A:GLY192 4.3 33.0 1.0 O A:CYS191 4.4 38.0 1.0 CB A:ASP270 4.5 38.3 1.0 CD A:ARG269 4.6 47.8 1.0 CB A:GLU273 4.6 39.6 1.0 N A:GLY192 4.8 31.8 1.0 C A:CYS191 4.8 36.8 1.0

Zinc binding site 2 out of 3 in the Human Cytochrome P450 2D6 Ajmalicine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Cytochrome P450 2D6 Ajmalicine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:54.0 occ:0.50 ND1 A:HIS426 2.1 58.2 1.0 OD2 A:ASP422 2.4 53.5 1.0 CE1 A:HIS426 3.1 61.0 1.0 CG A:HIS426 3.2 55.0 1.0 CG A:ASP422 3.2 49.8 1.0 OD1 A:ASP422 3.5 50.0 1.0 CB A:HIS426 3.5 50.8 1.0 CB A:GLN424 4.0 60.8 1.0 NE2 A:HIS426 4.2 61.1 1.0 CD2 A:HIS426 4.3 57.0 1.0 CG A:GLN424 4.5 67.5 1.0 CB A:ASP422 4.5 45.8 1.0 CA A:HIS426 4.7 50.6 1.0 N A:HIS426 4.8 53.8 1.0

Zinc binding site 3 out of 3 in the Human Cytochrome P450 2D6 Ajmalicine Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Cytochrome P450 2D6 Ajmalicine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:44.0 occ:1.00 OE2 B:GLU273 1.8 39.2 1.0 NE2 B:HIS258 2.1 36.0 1.0 OD2 B:ASP270 2.3 44.8 1.0 CD B:GLU273 2.7 39.7 1.0 CE1 B:HIS258 3.0 35.9 1.0 CD2 B:HIS258 3.2 36.3 1.0 CG B:ASP270 3.2 41.6 1.0 CG B:GLU273 3.2 39.9 1.0 OD1 B:ASP270 3.3 41.6 1.0 OE1 B:GLU273 3.7 40.1 1.0 ND1 B:HIS258 4.1 36.9 1.0 O B:HOH705 4.2 42.2 1.0 CG B:HIS258 4.2 36.8 1.0 NE B:ARG269 4.3 51.3 1.0 CB B:ARG269 4.4 47.2 1.0 O B:CYS191 4.4 42.3 1.0 CA B:GLY192 4.5 36.5 1.0 CB B:GLU273 4.5 37.8 1.0 CB B:ASP270 4.6 38.4 1.0 NH2 B:ARG269 4.6 48.3 1.0 C B:CYS191 4.8 39.8 1.0 N B:GLY192 4.9 36.5 1.0 CZ B:ARG269 4.9 49.2 1.0 N B:ASP270 5.0 38.9 1.0

A.Wang, C.D.Stout, Q.Zhang, E.F.Johnson. Contributions of Ionic Interactions and Protein Dynamics to Cytochrome P450 2D6 (CYP2D6)Substrate and Inhibitor Binding. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 25555909
DOI: 10.1074/JBC.M114.627661