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:
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: Fri Aug 9 10:30:12 2024
|