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Zinc in PDB 6csb: V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine

Enzymatic activity of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine

All present enzymatic activity of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine:
1.14.14.1;

Protein crystallography data

The structure of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine, PDB code: 6csb was solved by Y.T.Yang, K.Fujita, P.F.Wang, S.C.Im, N.M.Pearl, J.Meagher, J.Stuckey, L.Waskell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.47 / 2.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.738, 191.999, 250.460, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.9

Other elements in 6csb:

The structure of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine (pdb code 6csb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine, PDB code: 6csb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6csb

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Zinc binding site 1 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:38.4
occ:1.00
 NE2 A:HIS258 1.8 29.5 1.0
OE2 A:GLU273 2.0 30.0 1.0
OD2 A:ASP270 2.1 37.0 1.0
CE1 A:HIS258 2.6 34.0 1.0
CD A:GLU273 2.9 34.9 1.0
CD2 A:HIS258 3.0 45.0 1.0
CG A:ASP270 3.0 31.0 1.0
OD1 A:ASP270 3.3 30.2 1.0
CG A:GLU273 3.3 40.8 1.0
O A:CYS191 3.6 39.6 1.0
CG A:ARG269 3.7 78.1 1.0
ND1 A:HIS258 3.8 38.7 1.0
OE1 A:GLU273 3.9 38.8 1.0
CG A:HIS258 4.0 30.4 1.0
C A:CYS191 4.1 34.8 1.0
CD A:ARG269 4.2 0.4 1.0
O A:HOH713 4.2 43.7 1.0
NH1 A:ARG269 4.4 38.3 1.0
CB A:ASP270 4.4 29.1 1.0
CA A:GLY192 4.5 41.3 1.0
N A:GLY192 4.6 37.1 1.0
CB A:GLU273 4.6 32.3 1.0
CA A:CYS191 4.9 36.2 1.0
N A:ASP270 5.0 28.0 1.0

Zinc binding site 2 out of 9 in 6csb

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Zinc binding site 2 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:46.3
occ:1.00
 ND1 B:HIS426 1.8 47.5 1.0
OD2 A:ASP422 1.9 43.8 1.0
ND1 A:HIS426 1.9 50.3 1.0
OD2 B:ASP422 2.0 43.0 1.0
CE1 B:HIS426 2.6 57.0 1.0
CE1 A:HIS426 2.8 53.8 1.0
CG A:ASP422 2.9 42.9 1.0
CG A:HIS426 3.0 54.4 1.0
CG B:HIS426 3.0 59.8 1.0
CG B:ASP422 3.0 41.0 1.0
OD1 A:ASP422 3.3 39.6 1.0
CB A:HIS426 3.4 43.9 1.0
OD1 B:ASP422 3.5 42.1 1.0
CB B:HIS426 3.6 43.3 1.0
NE2 B:HIS426 3.8 57.8 1.0
NE2 A:HIS426 3.9 58.4 1.0
CB B:GLN424 4.0 49.9 1.0
O B:HOH839 4.0 40.6 1.0
CD2 B:HIS426 4.0 59.8 1.0
CD2 A:HIS426 4.0 53.6 1.0
CB A:GLN424 4.1 54.4 1.0
CB A:ASP422 4.2 40.6 1.0
CG A:GLN424 4.3 80.0 1.0
CB B:ASP422 4.3 38.1 1.0
CA A:HIS426 4.7 44.4 1.0
N A:HIS426 4.8 42.3 1.0
CG B:GLN424 4.8 72.2 1.0
CA B:HIS426 4.8 45.0 1.0
N B:HIS426 4.8 41.8 1.0
O B:HOH864 4.9 58.3 1.0

Zinc binding site 3 out of 9 in 6csb

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Zinc binding site 3 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn607

b:0.5
occ:1.00
 ND1 A:HIS463 2.5 93.1 1.0
NE2 A:HIS498 2.5 1.0 1.0
CD2 A:HIS498 3.1 0.1 1.0
CE1 A:HIS463 3.3 0.5 1.0
CG A:HIS463 3.3 75.7 1.0
CE1 A:HIS498 3.6 0.4 1.0
CB A:HIS463 3.6 50.8 1.0
CA A:HIS463 4.2 57.0 1.0
NE2 A:HIS463 4.3 97.8 1.0
CG A:HIS498 4.3 100.0 1.0
CD2 A:HIS463 4.3 93.6 1.0
ND1 A:HIS498 4.5 0.9 1.0
O A:HIS463 4.6 54.3 1.0
O A:GLN341 4.8 78.1 1.0
C A:HIS463 5.0 55.0 1.0

Zinc binding site 4 out of 9 in 6csb

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Zinc binding site 4 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn606

b:38.0
occ:1.00
 OE1 B:GLU273 1.8 20.0 1.0
NE2 B:HIS258 1.8 29.7 1.0
OD2 B:ASP270 2.0 34.0 1.0
CE1 B:HIS258 2.6 34.9 1.0
CD B:GLU273 2.7 31.6 1.0
CG B:ASP270 3.0 28.4 1.0
CD2 B:HIS258 3.0 40.1 1.0
OD1 B:ASP270 3.3 26.2 1.0
CG B:GLU273 3.3 30.0 1.0
O B:CYS191 3.5 40.4 1.0
ND1 B:HIS258 3.8 37.0 1.0
OE2 B:GLU273 3.8 29.9 1.0
CG B:ARG269 4.0 42.9 1.0
CG B:HIS258 4.0 28.1 1.0
O B:HOH769 4.1 37.1 1.0
C B:CYS191 4.1 31.1 1.0
O B:HOH724 4.2 46.2 1.0
NH1 B:ARG269 4.2 31.8 1.0
CB B:ASP270 4.3 30.4 1.0
CA B:GLY192 4.4 33.9 1.0
N B:GLY192 4.5 31.8 1.0
CD B:ARG269 4.5 49.9 1.0
CB B:GLU273 4.6 27.9 1.0
CA B:CYS191 4.9 30.3 1.0

Zinc binding site 5 out of 9 in 6csb

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Zinc binding site 5 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn607

b:0.0
occ:1.00
 CD2 B:HIS498 2.5 0.3 1.0
ND1 B:HIS463 2.5 85.1 1.0
NE2 B:HIS498 2.8 0.6 1.0
CE1 B:HIS463 3.3 84.0 1.0
CG B:HIS463 3.4 69.6 1.0
CB B:HIS463 3.7 50.3 1.0
CG B:HIS498 3.8 0.2 1.0
CE1 B:HIS498 4.2 0.1 1.0
CA B:HIS463 4.2 55.1 1.0
NE2 B:HIS463 4.3 80.5 1.0
CD2 B:HIS463 4.4 79.3 1.0
O B:HIS463 4.5 54.2 1.0
ND1 B:HIS498 4.6 0.9 1.0
O B:GLN341 4.7 80.7 1.0
CB B:HIS498 4.7 95.3 1.0
C B:HIS463 4.9 55.4 1.0

Zinc binding site 6 out of 9 in 6csb

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Zinc binding site 6 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn608

b:0.7
occ:1.00
 SG B:CYS493 3.1 51.7 1.0
OG1 B:THR470 4.2 87.0 1.0
O B:GLY169 4.2 78.4 1.0
CB B:CYS493 4.2 45.8 1.0
O B:HOH826 4.5 60.1 1.0
CG B:PRO171 4.5 66.1 1.0
N B:THR470 4.6 63.0 1.0
CD B:PRO171 4.8 67.8 1.0
CA B:PRO469 4.9 58.7 1.0

Zinc binding site 7 out of 9 in 6csb

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Zinc binding site 7 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn606

b:36.8
occ:1.00
 NE2 C:HIS258 1.8 29.9 1.0
OE2 C:GLU273 1.9 28.1 1.0
OD2 C:ASP270 1.9 39.5 1.0
CE1 C:HIS258 2.7 40.6 1.0
CG C:ASP270 2.9 37.9 1.0
CD C:GLU273 2.9 38.8 1.0
CD2 C:HIS258 3.0 35.9 1.0
OD1 C:ASP270 3.2 36.5 1.0
CG C:GLU273 3.4 37.3 1.0
O C:CYS191 3.6 45.3 1.0
ND1 C:HIS258 3.8 42.7 1.0
NE C:ARG269 3.9 48.2 0.5
OE1 C:GLU273 3.9 35.2 1.0
CG C:HIS258 4.0 31.3 1.0
CG C:ARG269 4.0 55.9 0.5
C C:CYS191 4.0 39.7 1.0
CG C:ARG269 4.2 55.5 0.5
CB C:ASP270 4.3 34.9 1.0
NH1 C:ARG269 4.3 40.7 0.5
NH1 C:ARG269 4.3 36.6 0.5
CA C:GLY192 4.3 47.2 1.0
N C:GLY192 4.4 36.3 1.0
CD C:ARG269 4.4 50.5 0.5
CZ C:ARG269 4.5 44.2 0.5
CB C:GLU273 4.6 34.0 1.0
CD C:ARG269 4.7 52.2 0.5
CA C:CYS191 4.9 39.0 1.0
N C:ASP270 5.0 36.5 1.0

Zinc binding site 8 out of 9 in 6csb

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Zinc binding site 8 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn607

b:0.0
occ:1.00
 SG C:CYS493 3.2 74.6 1.0
O C:HOH781 3.7 62.8 1.0
CB C:CYS493 3.9 64.0 1.0
OG1 C:THR470 4.7 77.8 1.0
CG2 C:THR470 4.7 83.8 1.0
N C:THR470 4.8 86.6 1.0

Zinc binding site 9 out of 9 in 6csb

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Zinc binding site 9 out of 9 in the V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of V308E Mutant of Cytochrome P450 2D6 Complexed with Thioridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn604

b:37.0
occ:1.00
 NE2 D:HIS258 1.8 34.0 1.0
OE2 D:GLU273 2.0 27.4 1.0
OD2 D:ASP270 2.0 36.5 1.0
CE1 D:HIS258 2.6 38.4 1.0
CD D:GLU273 2.8 33.0 1.0
CD2 D:HIS258 3.0 47.6 1.0
CG D:ASP270 3.0 32.6 1.0
OD1 D:ASP270 3.3 32.7 1.0
CG D:GLU273 3.3 38.9 1.0
O D:CYS191 3.7 36.3 1.0
ND1 D:HIS258 3.8 36.3 1.0
CG D:ARG269 3.8 52.9 1.0
OE1 D:GLU273 3.9 28.2 1.0
CG D:HIS258 4.0 32.8 1.0
C D:CYS191 4.2 36.7 1.0
O D:HOH753 4.3 47.9 1.0
CD D:ARG269 4.3 43.2 1.0
NH1 D:ARG269 4.3 29.5 1.0
CB D:ASP270 4.4 34.3 1.0
CA D:GLY192 4.5 38.3 1.0
CB D:GLU273 4.6 31.2 1.0
N D:GLY192 4.6 33.6 1.0
CA D:CYS191 5.0 34.0 1.0

Reference:

Y.T.Yang, F.Fujita, P.F.Wang, S.C.Im, N.M.Pearl, J.Meagher, J.Stuckey, L.Waskell. Characteristic Conformational Changes on the Distal and Proximal Surfaces of Cytochrome P450 2D6 in Response to Substrate Binding To Be Published.
Page generated: Mon Oct 28 19:06:15 2024

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