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Iron in PDB 3tbg: Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site

Enzymatic activity of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site

All present enzymatic activity of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site:
1.14.14.1;

Protein crystallography data

The structure of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site, PDB code: 3tbg 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) 36.90 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.190, 191.960, 249.480, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 24.7

Other elements in 3tbg:

The structure of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site (pdb code 3tbg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site, PDB code: 3tbg:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3tbg

Go back to Iron Binding Sites List in 3tbg
Iron binding site 1 out of 4 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:16.8
occ:1.00
 FE A:HEM800 0.0 16.8 1.0
NC A:HEM800 2.0 13.9 1.0
NA A:HEM800 2.1 13.8 1.0
NB A:HEM800 2.1 13.5 1.0
ND A:HEM800 2.1 17.3 1.0
SG A:CYS443 2.4 16.9 1.0
O A:HOH614 2.7 22.1 1.0
C1C A:HEM800 3.0 14.4 1.0
C1D A:HEM800 3.0 15.9 1.0
C4B A:HEM800 3.0 13.8 1.0
C4A A:HEM800 3.0 14.9 1.0
C4C A:HEM800 3.1 14.9 1.0
C1B A:HEM800 3.1 14.3 1.0
C1A A:HEM800 3.1 11.4 1.0
C4D A:HEM800 3.1 13.9 1.0
CHC A:HEM800 3.3 14.1 1.0
CHD A:HEM800 3.3 16.7 1.0
CHB A:HEM800 3.3 12.8 1.0
CHA A:HEM800 3.4 13.4 1.0
CB A:CYS443 3.4 17.8 1.0
CA A:CYS443 4.1 19.4 1.0
O A:ALA305 4.1 25.0 1.0
C2C A:HEM800 4.2 15.2 1.0
C2D A:HEM800 4.2 15.8 1.0
C3A A:HEM800 4.3 14.5 1.0
C3C A:HEM800 4.3 14.4 1.0
C3D A:HEM800 4.3 15.5 1.0
C2A A:HEM800 4.3 12.8 1.0
C3B A:HEM800 4.3 15.3 1.0
C2B A:HEM800 4.3 14.5 1.0
CB A:ALA305 4.6 24.3 1.0
N A:GLY445 4.8 17.8 1.0
C A:ALA305 4.8 23.5 1.0
C A:CYS443 4.9 18.6 1.0
O A:HOH615 4.9 40.5 1.0
N A:LEU444 5.0 15.8 1.0

Iron binding site 2 out of 4 in 3tbg

Go back to Iron Binding Sites List in 3tbg
Iron binding site 2 out of 4 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe800

b:18.5
occ:1.00
 FE B:HEM800 0.0 18.5 1.0
NC B:HEM800 2.0 18.2 1.0
NB B:HEM800 2.1 17.5 1.0
NA B:HEM800 2.1 17.9 1.0
ND B:HEM800 2.1 19.3 1.0
SG B:CYS443 2.3 22.8 1.0
O B:HOH589 2.6 27.2 1.0
C1C B:HEM800 3.0 19.3 1.0
C4B B:HEM800 3.0 18.5 1.0
C1B B:HEM800 3.0 19.3 1.0
C1D B:HEM800 3.0 18.0 1.0
C4A B:HEM800 3.1 18.4 1.0
C4D B:HEM800 3.1 17.2 1.0
C4C B:HEM800 3.1 18.6 1.0
C1A B:HEM800 3.1 16.7 1.0
CHC B:HEM800 3.3 16.8 1.0
CB B:CYS443 3.3 20.1 1.0
CHB B:HEM800 3.3 18.8 1.0
CHD B:HEM800 3.4 17.3 1.0
CHA B:HEM800 3.4 15.7 1.0
CA B:CYS443 4.0 20.8 1.0
O B:ALA305 4.1 27.7 1.0
C2C B:HEM800 4.2 20.0 1.0
C3B B:HEM800 4.2 19.0 1.0
C2D B:HEM800 4.3 18.0 1.0
C2B B:HEM800 4.3 17.9 1.0
C3A B:HEM800 4.3 16.4 1.0
C3C B:HEM800 4.3 18.6 1.0
C3D B:HEM800 4.3 18.3 1.0
C2A B:HEM800 4.3 17.4 1.0
CB B:ALA305 4.6 20.8 1.0
N B:GLY445 4.8 20.7 1.0
C B:CYS443 4.8 21.1 1.0
C B:ALA305 4.8 26.5 1.0
N B:LEU444 4.9 18.9 1.0

Iron binding site 3 out of 4 in 3tbg

Go back to Iron Binding Sites List in 3tbg
Iron binding site 3 out of 4 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe800

b:16.9
occ:1.00
 FE C:HEM800 0.0 16.9 1.0
NC C:HEM800 2.0 14.9 1.0
NA C:HEM800 2.1 13.8 1.0
NB C:HEM800 2.1 14.8 1.0
ND C:HEM800 2.1 16.6 1.0
SG C:CYS443 2.4 17.2 1.0
O C:HOH608 2.8 27.7 1.0
C1C C:HEM800 3.0 14.4 1.0
C4B C:HEM800 3.0 15.1 1.0
C1D C:HEM800 3.0 15.4 1.0
C4A C:HEM800 3.0 14.3 1.0
C1B C:HEM800 3.1 16.5 1.0
C4C C:HEM800 3.1 14.4 1.0
C1A C:HEM800 3.1 10.9 1.0
C4D C:HEM800 3.1 14.6 1.0
CHC C:HEM800 3.3 14.8 1.0
CB C:CYS443 3.3 15.4 1.0
CHB C:HEM800 3.3 14.2 1.0
CHD C:HEM800 3.3 15.1 1.0
CHA C:HEM800 3.4 12.7 1.0
CA C:CYS443 4.1 17.3 1.0
O C:ALA305 4.1 20.1 1.0
C2C C:HEM800 4.2 15.7 1.0
C2D C:HEM800 4.2 10.6 1.0
C3A C:HEM800 4.3 11.6 1.0
C3C C:HEM800 4.3 15.7 1.0
C3B C:HEM800 4.3 15.9 1.0
C3D C:HEM800 4.3 14.4 1.0
C2A C:HEM800 4.3 13.0 1.0
C2B C:HEM800 4.3 13.9 1.0
CB C:ALA305 4.7 20.4 1.0
N C:GLY445 4.8 20.1 1.0
C C:CYS443 4.8 18.2 1.0
C C:ALA305 4.9 21.4 1.0
N C:LEU444 4.9 18.1 1.0

Iron binding site 4 out of 4 in 3tbg

Go back to Iron Binding Sites List in 3tbg
Iron binding site 4 out of 4 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe800

b:21.6
occ:1.00
 FE D:HEM800 0.0 21.6 1.0
NC D:HEM800 2.1 21.9 1.0
NB D:HEM800 2.1 21.1 1.0
NA D:HEM800 2.1 21.8 1.0
ND D:HEM800 2.1 22.7 1.0
SG D:CYS443 2.3 20.9 1.0
C1C D:HEM800 3.0 22.6 1.0
C4B D:HEM800 3.0 22.5 1.0
C1D D:HEM800 3.0 21.5 1.0
C4A D:HEM800 3.0 22.0 1.0
C1B D:HEM800 3.0 22.9 1.0
C4D D:HEM800 3.1 21.4 1.0
C4C D:HEM800 3.1 22.6 1.0
C1A D:HEM800 3.1 21.7 1.0
O D:HOH587 3.1 35.6 1.0
CHC D:HEM800 3.3 22.4 1.0
CB D:CYS443 3.3 18.6 1.0
CHB D:HEM800 3.3 22.8 1.0
CHD D:HEM800 3.4 21.4 1.0
CHA D:HEM800 3.4 22.4 1.0
CA D:CYS443 4.1 21.5 1.0
O D:ALA305 4.2 27.0 1.0
C2D D:HEM800 4.2 20.4 1.0
C2C D:HEM800 4.2 24.3 1.0
C3B D:HEM800 4.3 23.5 1.0
C3A D:HEM800 4.3 22.1 1.0
C3D D:HEM800 4.3 22.2 1.0
C2B D:HEM800 4.3 21.9 1.0
C3C D:HEM800 4.3 23.4 1.0
C2A D:HEM800 4.3 22.3 1.0
CB D:ALA305 4.7 22.2 1.0
N D:GLY445 4.8 24.9 1.0
C D:ALA305 4.8 25.5 1.0
C D:CYS443 4.9 23.1 1.0
N D:LEU444 5.0 23.0 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. V. 290 5092 2015.
ISSN: ISSN 0021-9258
PubMed: 25555909
DOI: 10.1074/JBC.M114.627661
Page generated: Sun Aug 4 20:20:58 2024

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