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

Enzymatic activity of Human Cytochrome P450 2D6 Quinine Complex

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

Protein crystallography data

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

Other elements in 4wnv:

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

Iron (Fe) 4 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Cytochrome P450 2D6 Quinine Complex (pdb code 4wnv). 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 Quinine Complex, PDB code: 4wnv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4wnv

Go back to Zinc Binding Sites List in 4wnv
Zinc binding site 1 out of 7 in the Human Cytochrome P450 2D6 Quinine 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 Quinine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:24.1
occ:1.00
 NE2 A:HIS258 1.9 23.3 1.0
OE2 A:GLU273 1.9 18.7 1.0
OD2 A:ASP270 2.1 16.4 1.0
CE1 A:HIS258 2.7 23.2 1.0
CD A:GLU273 2.8 21.4 1.0
CG A:ASP270 2.9 16.3 1.0
CD2 A:HIS258 3.0 24.3 1.0
OD1 A:ASP270 3.2 16.2 1.0
CG A:GLU273 3.3 21.0 1.0
O A:CYS191 3.6 24.5 1.0
OE1 A:GLU273 3.8 18.8 1.0
ND1 A:HIS258 3.9 23.4 1.0
NE A:ARG269 4.0 34.8 1.0
CG A:HIS258 4.1 23.1 1.0
C A:CYS191 4.1 21.1 1.0
NH2 A:ARG269 4.3 35.2 1.0
CB A:ASP270 4.4 16.6 1.0
CB A:ARG269 4.4 27.9 1.0
CZ A:ARG269 4.6 36.9 1.0
N A:GLY192 4.6 19.7 1.0
CB A:GLU273 4.6 17.4 1.0
CA A:GLY192 4.6 18.9 1.0
CA A:CYS191 4.9 21.4 1.0
CD A:ARG269 4.9 33.5 1.0
N A:ASP270 4.9 17.7 1.0

Zinc binding site 2 out of 7 in 4wnv

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Zinc binding site 2 out of 7 in the Human Cytochrome P450 2D6 Quinine 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 Quinine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:53.5
occ:1.00
 ND1 A:HIS463 2.1 43.5 1.0
O A:HOH735 2.4 24.5 1.0
OE1 A:GLN341 2.7 67.6 1.0
CE1 A:HIS463 3.0 44.9 1.0
CG A:HIS463 3.2 40.4 1.0
CB A:HIS463 3.6 36.1 1.0
CA A:HIS463 3.8 34.8 1.0
CD A:GLN341 3.8 68.4 1.0
O A:HIS463 4.1 34.0 1.0
NE2 A:HIS463 4.2 43.4 1.0
NE2 A:GLN341 4.3 69.9 1.0
CD2 A:HIS463 4.3 41.5 1.0
O A:GLN341 4.4 50.4 1.0
O A:ARG497 4.5 42.9 1.0
C A:HIS463 4.5 33.5 1.0
O A:GLN462 4.9 37.4 1.0
N A:ARG497 4.9 39.7 1.0
N A:HIS463 5.0 33.4 1.0

Zinc binding site 3 out of 7 in 4wnv

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Zinc binding site 3 out of 7 in the Human Cytochrome P450 2D6 Quinine 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 Quinine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn607

b:28.9
occ:1.00
 OD1 C:ASP422 1.8 24.4 1.0
ND1 C:HIS426 1.9 31.9 1.0
ND1 A:HIS426 1.9 32.9 1.0
OD2 A:ASP422 2.0 25.9 1.0
CE1 C:HIS426 2.8 33.9 1.0
CE1 A:HIS426 2.9 35.8 1.0
CG C:ASP422 2.9 26.9 1.0
CG A:HIS426 3.0 31.8 1.0
CG A:ASP422 3.0 25.6 1.0
CG C:HIS426 3.0 30.8 1.0
OD1 A:ASP422 3.3 25.3 1.0
OD2 C:ASP422 3.3 24.3 1.0
CB A:HIS426 3.4 28.5 1.0
CB C:HIS426 3.5 27.8 1.0
NE2 A:HIS426 4.0 36.5 1.0
NE2 C:HIS426 4.0 34.5 1.0
CB A:GLN424 4.0 40.5 1.0
CD2 A:HIS426 4.1 34.3 1.0
CD2 C:HIS426 4.1 33.0 1.0
CB C:ASP422 4.2 22.6 1.0
CB A:ASP422 4.3 24.6 1.0
CB C:GLN424 4.4 40.4 1.0
CA A:HIS426 4.7 28.4 1.0
CG A:GLN424 4.7 44.9 1.0
N A:HIS426 4.7 30.1 1.0
CA C:HIS426 4.8 28.1 1.0
N C:HIS426 5.0 29.0 1.0

Zinc binding site 4 out of 7 in 4wnv

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Zinc binding site 4 out of 7 in the Human Cytochrome P450 2D6 Quinine Complex


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 Quinine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn605

b:28.2
occ:1.00
 NE2 B:HIS258 1.9 23.1 1.0
OE2 B:GLU273 2.0 24.4 1.0
OD2 B:ASP270 2.0 22.6 1.0
CE1 B:HIS258 2.8 26.8 1.0
CD B:GLU273 2.9 29.0 1.0
CG B:ASP270 2.9 21.4 1.0
CD2 B:HIS258 3.0 28.1 1.0
OD1 B:ASP270 3.1 21.3 1.0
CG B:GLU273 3.3 27.1 1.0
O B:CYS191 3.7 26.8 1.0
OE1 B:GLU273 3.9 24.6 1.0
ND1 B:HIS258 4.0 26.7 1.0
CG B:ARG269 4.0 34.2 1.0
CG B:HIS258 4.0 27.7 1.0
NH1 B:ARG269 4.2 33.2 1.0
C B:CYS191 4.2 24.3 1.0
CB B:ASP270 4.3 20.6 1.0
CD B:ARG269 4.4 36.9 1.0
CA B:GLY192 4.5 24.4 1.0
CB B:GLU273 4.6 23.2 1.0
N B:GLY192 4.6 24.0 1.0
N B:ASP270 5.0 25.4 1.0

Zinc binding site 5 out of 7 in 4wnv

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Zinc binding site 5 out of 7 in the Human Cytochrome P450 2D6 Quinine Complex


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 Quinine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn605

b:27.7
occ:1.00
 NE2 C:HIS258 1.9 23.9 1.0
OD2 C:ASP270 2.0 29.0 1.0
OE2 C:GLU273 2.0 25.9 1.0
CE1 C:HIS258 2.8 23.9 1.0
CD C:GLU273 2.9 25.9 1.0
CG C:ASP270 2.9 20.8 1.0
CD2 C:HIS258 2.9 26.7 1.0
OD1 C:ASP270 3.1 20.8 1.0
O C:CYS191 3.2 21.8 1.0
CG C:GLU273 3.4 23.4 1.0
C C:CYS191 3.9 21.1 1.0
NE C:ARG269 3.9 39.0 1.0
ND1 C:HIS258 4.0 23.6 1.0
OE1 C:GLU273 4.0 26.6 1.0
CG C:HIS258 4.0 25.4 1.0
NH2 C:ARG269 4.2 40.8 1.0
CB C:ASP270 4.3 22.7 1.0
CZ C:ARG269 4.4 41.2 1.0
N C:GLY192 4.6 23.6 1.0
CA C:GLY192 4.6 22.8 1.0
CA C:CYS191 4.6 21.4 1.0
CB C:ARG269 4.7 32.3 1.0
CB C:GLU273 4.7 24.4 1.0
CD C:ARG269 4.9 36.7 1.0

Zinc binding site 6 out of 7 in 4wnv

Go back to Zinc Binding Sites List in 4wnv
Zinc binding site 6 out of 7 in the Human Cytochrome P450 2D6 Quinine Complex


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 Quinine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn606

b:55.1
occ:1.00
 ND1 C:HIS463 2.2 40.2 1.0
OE1 C:GLN341 3.0 71.2 1.0
CE1 C:HIS463 3.1 42.0 1.0
CG C:HIS463 3.2 37.4 1.0
CB C:HIS463 3.5 34.3 1.0
CA C:HIS463 3.8 33.1 1.0
O C:HIS463 4.1 31.8 1.0
CD C:GLN341 4.2 70.6 1.0
NE2 C:HIS463 4.2 40.9 1.0
CD2 C:HIS463 4.3 38.5 1.0
O C:ARG497 4.4 46.1 1.0
C C:HIS463 4.5 31.5 1.0
O C:GLN341 4.8 65.3 1.0
CG C:GLN341 4.8 67.0 1.0
O C:GLN462 4.8 36.3 1.0
N C:ARG497 4.8 41.1 1.0
N C:HIS463 5.0 30.8 1.0

Zinc binding site 7 out of 7 in 4wnv

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Zinc binding site 7 out of 7 in the Human Cytochrome P450 2D6 Quinine Complex


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 Quinine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn604

b:28.3
occ:1.00
 NE2 D:HIS258 1.9 27.9 1.0
OD2 D:ASP270 2.0 24.2 1.0
OE1 D:GLU273 2.2 27.0 1.0
CE1 D:HIS258 2.8 29.4 1.0
CG D:ASP270 2.9 23.4 1.0
CD2 D:HIS258 3.0 29.0 1.0
CD D:GLU273 3.0 32.8 1.0
OD1 D:ASP270 3.2 23.4 1.0
CG D:GLU273 3.3 30.6 1.0
O D:CYS191 3.7 32.1 1.0
ND1 D:HIS258 3.9 29.8 1.0
NH1 D:ARG269 4.0 35.2 1.0
CG D:HIS258 4.0 29.1 1.0
CG D:ARG269 4.1 37.1 1.0
OE2 D:GLU273 4.1 33.6 1.0
C D:CYS191 4.1 30.1 1.0
O D:HOH705 4.2 39.1 1.0
CB D:ASP270 4.3 22.6 1.0
CD D:ARG269 4.5 39.0 1.0
N D:GLY192 4.5 28.2 1.0
CA D:GLY192 4.6 27.7 1.0
CB D:GLU273 4.7 29.3 1.0
CA D:CYS191 4.8 30.6 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: Sun Oct 27 10:01:58 2024

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