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Zinc in PDB 3tda: Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6

Enzymatic activity of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6

All present enzymatic activity of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6:
1.14.14.1;

Protein crystallography data

The structure of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6, PDB code: 3tda 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) 42.04 / 2.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.050, 192.740, 247.460, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.5

Other elements in 3tda:

The structure of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6 also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6 (pdb code 3tda). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6, PDB code: 3tda:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3tda

Go back to Zinc Binding Sites List in 3tda
Zinc binding site 1 out of 5 in the Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:29.6
occ:1.00
 OE2 A:GLU273 1.8 29.7 1.0
NE2 A:HIS258 2.0 26.2 1.0
OD2 A:ASP270 2.1 29.7 1.0
CE1 A:HIS258 2.7 26.2 1.0
CD A:GLU273 2.8 29.3 1.0
CG A:ASP270 3.0 29.4 1.0
CD2 A:HIS258 3.1 26.3 1.0
OD1 A:ASP270 3.3 28.6 1.0
CG A:GLU273 3.3 28.0 1.0
ND1 A:HIS258 3.9 27.6 1.0
OE1 A:GLU273 4.0 28.2 1.0
O A:HOH536 4.0 26.4 1.0
CG A:HIS258 4.1 27.0 1.0
CB A:ASP270 4.4 29.6 1.0
NE A:ARG269 4.4 36.3 1.0
CB A:ARG269 4.5 33.5 1.0
O A:CYS191 4.5 28.9 1.0
CB A:GLU273 4.5 27.6 1.0
CA A:GLY192 4.5 27.7 1.0
NH2 A:ARG269 4.7 33.9 1.0
N A:ASP270 4.8 31.0 1.0
CG A:ARG269 4.9 34.6 1.0
C A:CYS191 4.9 27.9 1.0
N A:GLY192 4.9 28.1 1.0

Zinc binding site 2 out of 5 in 3tda

Go back to Zinc Binding Sites List in 3tda
Zinc binding site 2 out of 5 in the Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:34.5
occ:1.00
 OD1 C:ASP422 1.9 32.3 1.0
OD2 A:ASP422 2.0 33.7 1.0
ND1 A:HIS426 2.1 38.8 1.0
ND1 C:HIS426 2.2 41.3 1.0
CG A:HIS426 2.9 38.2 1.0
CE1 A:HIS426 2.9 39.2 1.0
CG A:ASP422 3.0 31.8 1.0
CG C:HIS426 3.0 41.8 1.0
CE1 C:HIS426 3.0 42.3 1.0
CG C:ASP422 3.1 32.4 1.0
OD1 A:ASP422 3.3 28.6 1.0
CB A:HIS426 3.3 35.4 1.0
CB C:HIS426 3.4 39.3 1.0
OD2 C:ASP422 3.6 33.0 1.0
CB A:GLN424 3.8 41.7 1.0
NE2 A:HIS426 3.9 40.0 1.0
CD2 A:HIS426 3.9 38.6 1.0
NE2 C:HIS426 4.0 43.1 1.0
CB C:GLN424 4.0 44.5 1.0
CD2 C:HIS426 4.0 42.3 1.0
CG A:GLN424 4.2 45.6 1.0
CB C:ASP422 4.3 31.2 1.0
CB A:ASP422 4.3 31.3 1.0
CA A:HIS426 4.6 33.8 1.0
N A:HIS426 4.7 34.3 1.0
CA C:HIS426 4.8 38.1 1.0
CG C:GLN424 4.8 47.8 1.0
N C:HIS426 4.9 38.7 1.0

Zinc binding site 3 out of 5 in 3tda

Go back to Zinc Binding Sites List in 3tda
Zinc binding site 3 out of 5 in the Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn600

b:29.9
occ:1.00
 NE2 B:HIS258 1.8 27.7 1.0
OE1 B:GLU273 1.9 23.3 1.0
OD2 B:ASP270 2.0 37.1 1.0
CE1 B:HIS258 2.7 27.8 1.0
CD B:GLU273 2.8 24.6 1.0
CD2 B:HIS258 3.0 28.3 1.0
CG B:ASP270 3.0 35.6 1.0
CG B:GLU273 3.2 26.2 1.0
OD1 B:ASP270 3.4 36.3 1.0
ND1 B:HIS258 3.8 29.3 1.0
OE2 B:GLU273 3.9 24.3 1.0
CG B:HIS258 4.0 29.0 1.0
O B:HOH521 4.1 24.0 1.0
O B:CYS191 4.3 31.1 1.0
NE B:ARG269 4.4 40.1 1.0
CB B:ASP270 4.4 33.6 1.0
CB B:GLU273 4.6 27.7 1.0
CB B:ARG269 4.6 35.0 1.0
CA B:GLY192 4.6 32.1 1.0
NH2 B:ARG269 4.6 37.5 1.0
C B:CYS191 4.8 31.7 1.0
N B:ASP270 5.0 33.3 1.0
CZ B:ARG269 5.0 38.4 1.0
N B:GLY192 5.0 31.7 1.0

Zinc binding site 4 out of 5 in 3tda

Go back to Zinc Binding Sites List in 3tda
Zinc binding site 4 out of 5 in the Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:35.6
occ:1.00
 OE2 C:GLU273 1.8 32.2 1.0
NE2 C:HIS258 1.9 28.4 1.0
OD2 C:ASP270 1.9 36.4 1.0
CE1 C:HIS258 2.7 29.0 1.0
CD C:GLU273 2.8 32.5 1.0
CG C:ASP270 3.0 34.5 1.0
CD2 C:HIS258 3.0 29.6 1.0
CG C:GLU273 3.2 32.2 1.0
OD1 C:ASP270 3.4 35.7 1.0
OE1 C:GLU273 3.8 31.5 1.0
ND1 C:HIS258 3.9 30.8 1.0
CG C:ARG269 3.9 35.3 1.0
O C:HOH544 4.0 31.4 1.0
CG C:HIS258 4.0 29.5 1.0
NH1 C:ARG269 4.1 37.1 1.0
CB C:ASP270 4.2 33.2 1.0
O C:CYS191 4.3 33.8 1.0
CD C:ARG269 4.4 36.8 1.0
CB C:GLU273 4.4 31.6 1.0
CA C:GLY192 4.5 32.7 1.0
C C:CYS191 4.8 33.1 1.0
N C:ASP270 4.9 33.2 1.0
N C:GLY192 4.9 33.1 1.0

Zinc binding site 5 out of 5 in 3tda

Go back to Zinc Binding Sites List in 3tda
Zinc binding site 5 out of 5 in the Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Competitive Replacement of Thioridazine By Prinomastat in Crystals of Cytochrome P450 2D6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn600

b:34.0
occ:1.00
 NE2 D:HIS258 1.9 28.2 1.0
OE1 D:GLU273 2.0 28.1 1.0
OD2 D:ASP270 2.0 37.0 1.0
CE1 D:HIS258 2.8 28.5 1.0
CD D:GLU273 2.9 28.5 1.0
CD2 D:HIS258 3.0 29.5 1.0
CG D:ASP270 3.1 35.4 1.0
CG D:GLU273 3.2 28.8 1.0
OD1 D:ASP270 3.4 36.7 1.0
ND1 D:HIS258 3.9 30.1 1.0
OE2 D:GLU273 4.0 28.6 1.0
CG D:HIS258 4.0 29.9 1.0
CG D:ARG269 4.1 42.5 1.0
O D:CYS191 4.2 36.2 1.0
O D:HOH510 4.2 41.7 1.0
CD D:ARG269 4.3 45.5 1.0
NE D:ARG269 4.3 47.3 1.0
CB D:ASP270 4.4 33.7 1.0
CB D:GLU273 4.6 30.3 1.0
CA D:GLY192 4.6 32.5 1.0
C D:CYS191 4.8 35.3 1.0
OG1 D:THR261 5.0 36.1 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: Wed Dec 16 04:52:05 2020

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