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Sodium in PDB 4wnw: Human Cytochrome P450 2D6 Thioridazine Complex

Enzymatic activity of Human Cytochrome P450 2D6 Thioridazine Complex

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

Protein crystallography data

The structure of Human Cytochrome P450 2D6 Thioridazine Complex, PDB code: 4wnw 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) 32.98 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 194.190, 55.349, 145.223, 90.00, 134.19, 90.00
R / Rfree (%) 24.2 / 28.7

Other elements in 4wnw:

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

Nickel (Ni) 1 atom
Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Cytochrome P450 2D6 Thioridazine Complex (pdb code 4wnw). 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 Thioridazine Complex, PDB code: 4wnw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4wnw

Go back to Sodium Binding Sites List in 4wnw
Sodium binding site 1 out of 2 in the Human Cytochrome P450 2D6 Thioridazine 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 Thioridazine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:49.3
occ:1.00
OE2 A:GLU216 3.2 62.9 1.0
CD2 A:LEU121 4.0 33.1 1.0
CD A:GLU216 4.2 70.5 1.0
OE1 A:GLU216 4.3 61.6 1.0
OE1 A:GLN244 4.4 67.2 1.0
CD2 A:LEU241 4.6 50.2 1.0
CAA A:RTZ602 4.8 48.5 0.5
NE2 A:GLN244 4.9 53.3 1.0

Sodium binding site 2 out of 2 in 4wnw

Go back to Sodium Binding Sites List in 4wnw
Sodium binding site 2 out of 2 in the Human Cytochrome P450 2D6 Thioridazine 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 Thioridazine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:71.9
occ:1.00
OE2 B:GLU216 2.7 83.6 1.0
CD B:GLU216 3.4 81.2 1.0
NH2 B:ARG221 3.5 80.4 1.0
OE1 B:GLU216 3.5 75.6 1.0
CG2 B:THR107 3.7 71.4 1.0
CD1 B:LEU121 4.1 65.9 1.0
CD1 B:ILE106 4.1 72.7 1.0
NE B:ARG221 4.2 83.2 1.0
OE1 B:GLN244 4.3 70.7 1.0
CZ B:ARG221 4.3 86.1 1.0
CG1 B:ILE106 4.7 71.0 1.0
CG1 B:VAL104 4.8 68.0 1.0
NE2 B:GLN244 4.8 76.8 1.0
CG B:GLU216 4.8 74.5 1.0
CD B:GLN244 5.0 75.5 1.0

Reference:

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
Page generated: Tue Dec 15 09:38:35 2020

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