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Zinc 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:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 7 binding sites of Zinc where determined in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site, PDB code: 3tbg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3tbg

Go back to Zinc Binding Sites List in 3tbg
Zinc binding site 1 out of 7 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


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 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:21.4
occ:1.00
 OE2 A:GLU273 1.9 16.2 1.0
NE2 A:HIS258 2.0 18.4 1.0
OD2 A:ASP270 2.0 20.9 1.0
CE1 A:HIS258 2.8 24.3 1.0
CD A:GLU273 2.8 19.3 1.0
CG A:ASP270 2.9 18.8 1.0
CD2 A:HIS258 3.1 22.8 1.0
OD1 A:ASP270 3.2 17.2 1.0
CG A:GLU273 3.3 18.9 1.0
O A:CYS191 3.6 25.7 1.0
OE1 A:GLU273 3.8 18.3 1.0
ND1 A:HIS258 4.0 25.5 1.0
O A:HOH586 4.1 33.3 1.0
CG A:HIS258 4.1 23.6 1.0
C A:CYS191 4.2 24.6 1.0
O A:HOH581 4.2 30.2 1.0
CB A:ASP270 4.3 21.6 1.0
NE A:ARG269 4.4 38.9 1.0
NH2 A:ARG269 4.4 32.6 1.0
CA A:GLY192 4.5 22.6 1.0
CB A:GLU273 4.6 17.4 1.0
CB A:ARG269 4.6 29.2 1.0
N A:GLY192 4.6 24.4 1.0
N A:ASP270 4.8 20.7 1.0
CZ A:ARG269 4.9 36.4 1.0
CA A:CYS191 5.0 27.1 1.0

Zinc binding site 2 out of 7 in 3tbg

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Zinc binding site 2 out of 7 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


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 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:27.7
occ:1.00
 ND1 A:HIS426 1.8 35.5 1.0
ND1 C:HIS426 1.9 31.2 1.0
OD1 C:ASP422 2.0 26.1 1.0
OD2 A:ASP422 2.2 26.2 1.0
CE1 A:HIS426 2.7 36.5 1.0
CE1 C:HIS426 2.8 33.3 1.0
CG C:HIS426 2.9 32.7 1.0
CG A:HIS426 2.9 33.6 1.0
CG C:ASP422 3.0 23.0 1.0
CG A:ASP422 3.1 23.9 1.0
CB C:HIS426 3.4 28.5 1.0
OD1 A:ASP422 3.4 21.7 1.0
OD2 C:ASP422 3.4 22.4 1.0
CB A:HIS426 3.5 26.8 1.0
NE2 A:HIS426 3.8 36.9 1.0
NE2 C:HIS426 3.9 34.1 1.0
CB C:GLN424 3.9 38.4 1.0
CD2 A:HIS426 4.0 32.2 1.0
CD2 C:HIS426 4.0 32.6 1.0
CB A:GLN424 4.0 37.0 1.0
O A:HOH564 4.2 28.2 1.0
CB C:ASP422 4.2 26.1 1.0
CB A:ASP422 4.3 25.3 1.0
CG C:GLN424 4.5 44.9 1.0
CA C:HIS426 4.7 27.5 1.0
CG A:GLN424 4.7 42.2 1.0
CA A:HIS426 4.7 25.8 1.0
N C:HIS426 4.8 28.3 1.0
N A:HIS426 4.8 26.2 1.0

Zinc binding site 3 out of 7 in 3tbg

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Zinc binding site 3 out of 7 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


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 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:91.0
occ:1.00
 ND1 A:HIS463 2.7 47.3 1.0
CG A:HIS463 3.6 45.7 1.0
CE1 A:HIS463 3.7 48.7 1.0
CB A:HIS463 3.8 40.9 1.0
CA A:HIS463 3.9 38.3 1.0
O A:HIS463 4.1 36.6 1.0
O A:ARG497 4.3 47.8 1.0
C A:HIS463 4.5 36.9 1.0
O A:GLN341 4.6 49.9 1.0
O A:GLN462 4.7 38.5 1.0
NE2 A:HIS463 4.8 49.1 1.0
CD2 A:HIS463 4.8 46.9 1.0
N A:ARG497 4.8 42.7 1.0
N A:HIS463 5.0 38.1 1.0

Zinc binding site 4 out of 7 in 3tbg

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Zinc binding site 4 out of 7 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn600

b:23.9
occ:1.00
 OE2 B:GLU273 1.9 14.9 1.0
NE2 B:HIS258 1.9 21.6 1.0
OD2 B:ASP270 2.0 24.1 1.0
CE1 B:HIS258 2.8 26.5 1.0
CD B:GLU273 2.8 19.1 1.0
CG B:ASP270 3.0 22.1 1.0
CD2 B:HIS258 3.0 24.5 1.0
OD1 B:ASP270 3.3 20.5 1.0
CG B:GLU273 3.4 18.4 1.0
O B:CYS191 3.5 28.0 1.0
OE1 B:GLU273 3.9 19.0 1.0
ND1 B:HIS258 3.9 26.4 1.0
NE B:ARG269 3.9 44.9 1.0
CG B:ARG269 4.0 36.2 1.0
CG B:HIS258 4.0 24.8 1.0
C B:CYS191 4.2 27.8 1.0
CB B:ASP270 4.3 24.3 1.0
CD B:ARG269 4.3 38.8 1.0
CA B:GLY192 4.5 26.1 1.0
CB B:GLU273 4.6 17.7 1.0
N B:GLY192 4.6 26.6 1.0
CZ B:ARG269 4.8 40.6 1.0
NH2 B:ARG269 4.9 39.4 1.0
N B:ASP270 4.9 23.3 1.0

Zinc binding site 5 out of 7 in 3tbg

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Zinc binding site 5 out of 7 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:24.4
occ:1.00
 OE2 C:GLU273 1.8 20.0 1.0
NE2 C:HIS258 1.9 19.3 1.0
OD2 C:ASP270 2.0 20.2 1.0
CE1 C:HIS258 2.8 27.0 1.0
CD C:GLU273 2.8 21.3 1.0
CG C:ASP270 2.9 22.5 1.0
CD2 C:HIS258 3.0 26.6 1.0
OD1 C:ASP270 3.2 23.7 1.0
CG C:GLU273 3.4 20.5 1.0
O C:CYS191 3.6 23.3 1.0
OE1 C:GLU273 3.8 20.1 1.0
ND1 C:HIS258 3.9 26.9 1.0
NE C:ARG269 4.0 39.7 1.0
CG C:HIS258 4.1 25.3 1.0
CG C:ARG269 4.1 33.5 1.0
C C:CYS191 4.1 23.2 1.0
O C:HOH529 4.2 36.4 1.0
CB C:ASP270 4.3 22.1 1.0
CD C:ARG269 4.5 35.1 1.0
CA C:GLY192 4.6 23.1 1.0
CB C:GLU273 4.6 19.0 1.0
N C:GLY192 4.6 24.7 1.0
CZ C:ARG269 4.8 34.9 1.0
NH2 C:ARG269 4.9 33.5 1.0
CA C:CYS191 5.0 25.0 1.0
N C:ASP270 5.0 24.0 1.0

Zinc binding site 6 out of 7 in 3tbg

Go back to Zinc Binding Sites List in 3tbg
Zinc binding site 6 out of 7 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:79.9
occ:1.00
 ND1 C:HIS463 2.4 47.4 1.0
CE1 C:HIS463 3.2 48.5 1.0
NE2 C:GLN341 3.4 62.7 1.0
CG C:HIS463 3.4 44.8 1.0
CB C:HIS463 3.8 41.0 1.0
CA C:HIS463 3.9 38.8 1.0
CG C:GLN341 4.2 60.4 1.0
CD C:GLN341 4.2 62.3 1.0
O C:HIS463 4.3 38.4 1.0
NE2 C:HIS463 4.4 50.3 1.0
O C:GLN341 4.5 54.9 1.0
CD2 C:HIS463 4.5 47.5 1.0
O C:ARG497 4.5 48.2 1.0
C C:HIS463 4.6 37.5 1.0
O C:GLN462 4.7 40.1 1.0
N C:ARG497 4.9 43.8 1.0
N C:HIS463 4.9 38.5 1.0

Zinc binding site 7 out of 7 in 3tbg

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Zinc binding site 7 out of 7 in the Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Cytochrome P450 2D6 with Two Thioridazines Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn600

b:26.3
occ:1.00
 OE1 D:GLU273 1.9 20.0 1.0
OD2 D:ASP270 1.9 23.9 1.0
NE2 D:HIS258 2.0 18.7 1.0
CD D:GLU273 2.8 22.8 1.0
CE1 D:HIS258 2.9 26.6 1.0
CG D:ASP270 2.9 23.8 1.0
CD2 D:HIS258 3.0 27.6 1.0
OD1 D:ASP270 3.2 24.2 1.0
CG D:GLU273 3.3 22.1 1.0
O D:CYS191 3.6 28.1 1.0
OE2 D:GLU273 3.9 20.3 1.0
NE D:ARG269 4.0 44.5 1.0
ND1 D:HIS258 4.0 27.3 1.0
CG D:HIS258 4.1 26.2 1.0
C D:CYS191 4.2 27.5 1.0
CG D:ARG269 4.2 39.3 1.0
CB D:ASP270 4.3 23.3 1.0
CA D:GLY192 4.5 24.3 1.0
CD D:ARG269 4.6 39.2 1.0
NH2 D:ARG269 4.6 36.9 1.0
CZ D:ARG269 4.6 40.5 1.0
N D:GLY192 4.6 25.9 1.0
CB D:GLU273 4.6 20.2 1.0
N D:ASP270 4.9 26.7 1.0
CA D:CYS191 5.0 30.0 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: Sat Oct 26 16:28:31 2024

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