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Iron in PDB 7wy4: Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene

Enzymatic activity of Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene

All present enzymatic activity of Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene:
1.14.14.1; 1.6.2.4;

Protein crystallography data

The structure of Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene, PDB code: 7wy4 was solved by K.Suzuki, J.K.Stanfield, Y.Shisaka, K.Omura, C.Kasai, H.Sugimoto, O.Shoji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.22 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.97, 126.65, 148.75, 90, 90, 90
R / Rfree (%) 14.3 / 17.9

Other elements in 7wy4:

The structure of Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene (pdb code 7wy4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene, PDB code: 7wy4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7wy4

Go back to Iron Binding Sites List in 7wy4
Iron binding site 1 out of 4 in the Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:10.0
occ:0.50
 FE A:HEM501 0.0 10.0 0.5
FE A:HEM501 0.0 13.7 0.5
ND A:HEM501 1.9 10.8 0.5
ND A:HEM501 1.9 11.1 0.5
NA A:HEM501 2.0 10.3 0.5
NA A:HEM501 2.0 11.0 0.5
NC A:HEM501 2.1 8.2 0.5
NB A:HEM501 2.1 11.8 0.5
NC A:HEM501 2.1 11.0 0.5
NB A:HEM501 2.1 10.8 0.5
SG A:CYS400 2.4 12.2 1.0
C1D A:HEM501 3.0 10.3 0.5
C1D A:HEM501 3.0 11.2 0.5
C4D A:HEM501 3.0 10.6 0.5
C4D A:HEM501 3.0 10.6 0.5
C4B A:HEM501 3.0 11.6 0.5
C4C A:HEM501 3.0 9.7 0.5
C4C A:HEM501 3.0 10.7 0.5
C1A A:HEM501 3.0 10.3 0.5
C4B A:HEM501 3.0 11.6 0.5
C1A A:HEM501 3.1 10.0 0.5
C1B A:HEM501 3.1 11.1 0.5
C1C A:HEM501 3.1 9.8 0.5
C1C A:HEM501 3.1 11.4 0.5
C4A A:HEM501 3.1 10.4 0.5
C1B A:HEM501 3.1 11.8 0.5
C4A A:HEM501 3.1 11.3 0.5
CB A:CYS400 3.3 11.1 1.0
CHD A:HEM501 3.4 9.8 0.5
CHD A:HEM501 3.4 11.2 0.5
CHA A:HEM501 3.4 11.4 0.5
CHC A:HEM501 3.4 11.7 0.5
CHA A:HEM501 3.4 10.5 0.5
CHC A:HEM501 3.4 10.7 0.5
CHB A:HEM501 3.5 10.3 0.5
CHB A:HEM501 3.5 11.7 0.5
CAD A:SYN503 4.0 33.2 1.0
CA A:CYS400 4.0 10.6 1.0
CAC A:SYN503 4.0 28.1 1.0
C3C A:HEM501 4.2 11.3 0.5
C2C A:HEM501 4.2 11.1 0.5
C3C A:HEM501 4.2 11.0 0.5
C2D A:HEM501 4.2 10.6 0.5
C2D A:HEM501 4.3 10.0 0.5
C3D A:HEM501 4.3 11.1 0.5
C2C A:HEM501 4.3 11.8 0.5
C2A A:HEM501 4.3 9.7 0.5
C3A A:HEM501 4.3 11.1 0.5
C3D A:HEM501 4.3 11.0 0.5
C2B A:HEM501 4.3 11.4 0.5
C2A A:HEM501 4.3 10.1 0.5
C3A A:HEM501 4.3 9.3 0.5
C3B A:HEM501 4.3 11.7 0.5
C2B A:HEM501 4.3 13.4 0.5
C3B A:HEM501 4.3 13.2 0.5
N A:GLY402 4.7 11.5 1.0
C A:CYS400 4.8 11.2 1.0
N A:ILE401 4.9 10.3 1.0

Iron binding site 2 out of 4 in 7wy4

Go back to Iron Binding Sites List in 7wy4
Iron binding site 2 out of 4 in the Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:13.7
occ:0.50
 FE A:HEM501 0.0 13.7 0.5
FE A:HEM501 0.0 10.0 0.5
ND A:HEM501 1.9 11.1 0.5
ND A:HEM501 1.9 10.8 0.5
NA A:HEM501 2.0 10.3 0.5
NA A:HEM501 2.0 11.0 0.5
NC A:HEM501 2.1 8.2 0.5
NC A:HEM501 2.1 11.0 0.5
NB A:HEM501 2.1 11.8 0.5
NB A:HEM501 2.1 10.8 0.5
SG A:CYS400 2.4 12.2 1.0
C1D A:HEM501 3.0 11.2 0.5
C4D A:HEM501 3.0 10.6 0.5
C1D A:HEM501 3.0 10.3 0.5
C4D A:HEM501 3.0 10.6 0.5
C1A A:HEM501 3.0 10.3 0.5
C4C A:HEM501 3.0 10.7 0.5
C4B A:HEM501 3.0 11.6 0.5
C4C A:HEM501 3.0 9.7 0.5
C1A A:HEM501 3.1 10.0 0.5
C4B A:HEM501 3.1 11.6 0.5
C4A A:HEM501 3.1 11.3 0.5
C1B A:HEM501 3.1 11.1 0.5
C1B A:HEM501 3.1 11.8 0.5
C1C A:HEM501 3.1 9.8 0.5
C1C A:HEM501 3.1 11.4 0.5
C4A A:HEM501 3.1 10.4 0.5
CB A:CYS400 3.3 11.1 1.0
CHD A:HEM501 3.4 11.2 0.5
CHA A:HEM501 3.4 11.4 0.5
CHA A:HEM501 3.4 10.5 0.5
CHD A:HEM501 3.4 9.8 0.5
CHC A:HEM501 3.5 11.7 0.5
CHC A:HEM501 3.5 10.7 0.5
CHB A:HEM501 3.5 10.3 0.5
CHB A:HEM501 3.5 11.7 0.5
CA A:CYS400 3.9 10.6 1.0
CAD A:SYN503 4.0 33.2 1.0
CAC A:SYN503 4.0 28.1 1.0
C2D A:HEM501 4.2 10.6 0.5
C3C A:HEM501 4.2 11.3 0.5
C3C A:HEM501 4.2 11.0 0.5
C3D A:HEM501 4.2 11.1 0.5
C2A A:HEM501 4.2 9.7 0.5
C3A A:HEM501 4.3 11.1 0.5
C2D A:HEM501 4.3 10.0 0.5
C2C A:HEM501 4.3 11.1 0.5
C2C A:HEM501 4.3 11.8 0.5
C3D A:HEM501 4.3 11.0 0.5
C2A A:HEM501 4.3 10.1 0.5
C3A A:HEM501 4.3 9.3 0.5
C2B A:HEM501 4.3 13.4 0.5
C2B A:HEM501 4.3 11.4 0.5
C3B A:HEM501 4.3 11.7 0.5
C3B A:HEM501 4.3 13.2 0.5
N A:GLY402 4.7 11.5 1.0
C A:CYS400 4.7 11.2 1.0
N A:ILE401 4.9 10.3 1.0

Iron binding site 3 out of 4 in 7wy4

Go back to Iron Binding Sites List in 7wy4
Iron binding site 3 out of 4 in the Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:13.3
occ:0.50
 FE B:HEM501 0.0 13.3 0.5
FE B:HEM501 0.0 11.3 0.5
ND B:HEM501 1.9 12.7 0.5
ND B:HEM501 1.9 10.4 0.5
NA B:HEM501 2.0 14.1 0.5
NA B:HEM501 2.0 11.5 0.5
NC B:HEM501 2.1 11.1 0.5
NC B:HEM501 2.1 11.1 0.5
NB B:HEM501 2.1 12.2 0.5
NB B:HEM501 2.1 13.2 0.5
SG B:CYS400 2.4 13.7 1.0
C1D B:HEM501 3.0 12.5 0.5
C1D B:HEM501 3.0 8.9 0.5
C4D B:HEM501 3.0 13.4 0.5
C4D B:HEM501 3.0 9.6 0.5
C1A B:HEM501 3.0 14.5 0.5
C4B B:HEM501 3.0 12.6 0.5
C4B B:HEM501 3.0 13.4 0.5
C4C B:HEM501 3.0 11.1 0.5
C4C B:HEM501 3.0 12.1 0.5
C1A B:HEM501 3.1 9.7 0.5
C4A B:HEM501 3.1 15.1 0.5
C1B B:HEM501 3.1 15.2 0.5
C1C B:HEM501 3.1 11.0 0.5
C1C B:HEM501 3.1 12.4 0.5
C1B B:HEM501 3.1 11.7 0.5
C4A B:HEM501 3.1 10.5 0.5
CB B:CYS400 3.3 11.8 1.0
CHD B:HEM501 3.4 11.8 0.5
CHD B:HEM501 3.4 9.8 0.5
CHA B:HEM501 3.4 14.6 0.5
CHC B:HEM501 3.4 12.3 0.5
CHC B:HEM501 3.4 13.2 0.5
CHA B:HEM501 3.4 9.6 0.5
CHB B:HEM501 3.5 15.1 0.5
CHB B:HEM501 3.5 11.1 0.5
CA B:CYS400 4.0 11.9 1.0
CAD B:SYN503 4.0 36.2 0.7
C2D B:HEM501 4.2 12.8 0.5
C2A B:HEM501 4.2 15.5 0.5
C3C B:HEM501 4.2 13.6 0.5
C3A B:HEM501 4.2 16.7 0.5
C3C B:HEM501 4.2 10.9 0.5
C3D B:HEM501 4.3 13.8 0.5
C2D B:HEM501 4.3 8.3 0.5
C2C B:HEM501 4.3 12.3 0.5
C2C B:HEM501 4.3 10.6 0.5
CAC B:SYN503 4.3 35.1 0.7
C3D B:HEM501 4.3 10.0 0.5
C2A B:HEM501 4.3 10.0 0.5
C3A B:HEM501 4.3 10.1 0.5
C2B B:HEM501 4.3 15.8 0.5
C3B B:HEM501 4.3 11.5 0.5
C3B B:HEM501 4.3 14.9 0.5
C2B B:HEM501 4.3 11.5 0.5
O B:ALA264 4.5 18.2 0.5
CAC B:SYN503 4.6 29.0 0.3
N B:GLY402 4.7 12.9 1.0
CB B:ALA264 4.7 18.2 0.5
C B:CYS400 4.8 12.4 1.0
CAE B:SYN503 4.9 29.6 0.3
N B:ILE401 4.9 11.4 1.0
C B:ALA264 4.9 16.9 0.5

Iron binding site 4 out of 4 in 7wy4

Go back to Iron Binding Sites List in 7wy4
Iron binding site 4 out of 4 in the Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Styrene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.3
occ:0.50
 FE B:HEM501 0.0 11.3 0.5
FE B:HEM501 0.0 13.3 0.5
ND B:HEM501 1.9 12.7 0.5
ND B:HEM501 1.9 10.4 0.5
NA B:HEM501 2.0 14.1 0.5
NA B:HEM501 2.0 11.5 0.5
NC B:HEM501 2.0 11.1 0.5
NB B:HEM501 2.1 12.2 0.5
NC B:HEM501 2.1 11.1 0.5
NB B:HEM501 2.1 13.2 0.5
SG B:CYS400 2.4 13.7 1.0
C1D B:HEM501 3.0 12.5 0.5
C4D B:HEM501 3.0 13.4 0.5
C1D B:HEM501 3.0 8.9 0.5
C4D B:HEM501 3.0 9.6 0.5
C4B B:HEM501 3.0 12.6 0.5
C4C B:HEM501 3.0 12.1 0.5
C4B B:HEM501 3.0 13.4 0.5
C1A B:HEM501 3.0 14.5 0.5
C4C B:HEM501 3.0 11.1 0.5
C1A B:HEM501 3.1 9.7 0.5
C1C B:HEM501 3.1 12.4 0.5
C1B B:HEM501 3.1 11.7 0.5
C1C B:HEM501 3.1 11.0 0.5
C1B B:HEM501 3.1 15.2 0.5
C4A B:HEM501 3.1 10.5 0.5
C4A B:HEM501 3.1 15.1 0.5
CB B:CYS400 3.4 11.8 1.0
CHD B:HEM501 3.4 11.8 0.5
CHC B:HEM501 3.4 12.3 0.5
CHC B:HEM501 3.4 13.2 0.5
CHD B:HEM501 3.4 9.8 0.5
CHA B:HEM501 3.4 14.6 0.5
CHA B:HEM501 3.5 9.6 0.5
CHB B:HEM501 3.5 11.1 0.5
CHB B:HEM501 3.5 15.1 0.5
CA B:CYS400 4.0 11.9 1.0
CAD B:SYN503 4.0 36.2 0.7
C3C B:HEM501 4.2 13.6 0.5
C2D B:HEM501 4.2 12.8 0.5
C2C B:HEM501 4.2 12.3 0.5
C3C B:HEM501 4.2 10.9 0.5
CAC B:SYN503 4.3 35.1 0.7
C3D B:HEM501 4.3 13.8 0.5
C2A B:HEM501 4.3 15.5 0.5
C2C B:HEM501 4.3 10.6 0.5
C3A B:HEM501 4.3 16.7 0.5
C2D B:HEM501 4.3 8.3 0.5
C3A B:HEM501 4.3 10.1 0.5
C2A B:HEM501 4.3 10.0 0.5
C3B B:HEM501 4.3 11.5 0.5
C3D B:HEM501 4.3 10.0 0.5
C2B B:HEM501 4.3 11.5 0.5
C2B B:HEM501 4.3 15.8 0.5
C3B B:HEM501 4.3 14.9 0.5
O B:ALA264 4.5 18.2 0.5
CAC B:SYN503 4.6 29.0 0.3
N B:GLY402 4.7 12.9 1.0
CB B:ALA264 4.7 18.2 0.5
C B:CYS400 4.8 12.4 1.0
CAE B:SYN503 4.9 29.6 0.3
N B:ILE401 4.9 11.4 1.0
C B:ALA264 4.9 16.9 0.5

Reference:

K.Suzuki, J.K.Stanfield, K.Omura, Y.Shisaka, S.Ariyasu, C.Kasai, Y.Aiba, H.Sugimoto, O.Shoji. A Compound I Mimic Reveals the Transient Active Species of A Cytochrome P450 Enzyme: Insight Into the Stereoselectivity of P450-Catalysed Oxidations. Angew.Chem.Int.Ed.Engl. 2022.
ISSN: ESSN 1521-3773
PubMed: 36519803
DOI: 10.1002/ANIE.202215706
Page generated: Wed Apr 5 07:01:51 2023

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