Sodium in PDB 4wnv: Human Cytochrome P450 2D6 Quinine Complex

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

The structure of Human Cytochrome P450 2D6 Quinine Complex, PDB code: 4wnv 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)	35.43 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.569, 192.699, 249.588, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.8

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

Iron	(Fe)	4 atoms
Zinc	(Zn)	7 atoms

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

Sodium binding site 1 out of 2 in the Human Cytochrome P450 2D6 Quinine Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Cytochrome P450 2D6 Quinine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:55.2 occ:1.00 OE2 B:GLU130 2.5 29.5 1.0 OG B:SER288 2.7 26.7 1.0 CD1 B:PHE290 3.3 25.0 1.0 CD B:GLU130 3.4 28.4 1.0 CB B:SER288 3.4 28.0 1.0 CE1 B:PHE290 3.6 23.2 1.0 OE1 B:GLU130 3.7 24.6 1.0 CA B:SER288 4.0 33.4 1.0 CG B:PHE290 4.5 25.8 1.0 CB B:ALA282 4.5 28.7 1.0 N B:SER289 4.6 25.6 1.0 ND2 B:ASN285 4.6 31.5 1.0 CG B:GLU130 4.7 27.7 1.0 C B:SER288 4.8 30.0 1.0 CB B:PHE290 4.9 24.4 1.0 N B:PHE290 4.9 24.5 1.0

Sodium binding site 2 out of 2 in the Human Cytochrome P450 2D6 Quinine Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Cytochrome P450 2D6 Quinine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na605 b:30.7 occ:1.00 N D:PHE436 2.7 15.2 1.0 O D:SER437 2.8 18.4 1.0 O D:HOH730 2.9 32.3 1.0 C D:LEU434 3.1 16.4 1.0 CA D:PHE436 3.2 19.0 1.0 CB D:PHE436 3.2 18.5 1.0 CA D:LEU434 3.2 17.2 1.0 N D:SER437 3.2 19.4 1.0 C D:PHE436 3.3 19.6 1.0 N D:PRO435 3.4 15.7 1.0 O D:LEU434 3.6 16.1 1.0 CD2 D:LEU434 3.6 20.7 1.0 CD D:PRO435 3.7 15.8 1.0 O D:HOH729 3.7 45.2 1.0 C D:SER437 3.8 18.4 1.0 C D:PRO435 3.9 17.0 1.0 O D:PHE433 4.0 18.4 1.0 CB D:LEU434 4.0 19.0 1.0 CA D:SER437 4.0 18.4 1.0 CD1 D:PHE436 4.1 19.5 1.0 CG D:PHE436 4.1 19.0 1.0 O D:PHE436 4.1 20.2 1.0 CA D:PRO435 4.2 15.3 1.0 N D:LEU434 4.3 17.6 1.0 CG D:PRO435 4.4 15.3 1.0 CG D:LEU434 4.4 22.2 1.0 C D:PHE433 4.6 18.6 1.0 OE2 D:GLU446 4.7 25.9 1.0 O D:PRO435 4.9 16.1 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