Iron in PDB 7d0u: Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine
Enzymatic activity of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine
All present enzymatic activity of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine:
1.14.14.1;
1.6.2.4;
Protein crystallography data
The structure of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine, PDB code: 7d0u
was solved by
J.K.Stanfield,
H.Sugimoto,
O.Shoji,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.66 /
1.68
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.897,
128.581,
148.938,
90,
90,
90
|
R / Rfree (%)
|
18.6 /
21.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine
(pdb code 7d0u). 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 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine, PDB code: 7d0u:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7d0u
Go back to
Iron Binding Sites List in 7d0u
Iron binding site 1 out
of 4 in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine
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 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:16.4
occ:0.50
|
FE
|
A:HEM501
|
0.0
|
16.4
|
0.5
|
FE
|
A:HEM501
|
0.1
|
16.4
|
0.5
|
ND
|
A:HEM501
|
1.9
|
15.7
|
0.5
|
NA
|
A:HEM501
|
2.0
|
15.3
|
0.5
|
ND
|
A:HEM501
|
2.0
|
16.4
|
0.5
|
NA
|
A:HEM501
|
2.0
|
16.5
|
0.5
|
NB
|
A:HEM501
|
2.0
|
15.4
|
0.5
|
NB
|
A:HEM501
|
2.0
|
16.0
|
0.5
|
NC
|
A:HEM501
|
2.1
|
16.8
|
0.5
|
NC
|
A:HEM501
|
2.1
|
15.2
|
0.5
|
N
|
A:NEH503
|
2.2
|
19.6
|
1.0
|
SG
|
A:CYS400
|
2.3
|
16.7
|
1.0
|
C1D
|
A:HEM501
|
2.9
|
15.8
|
0.5
|
C4D
|
A:HEM501
|
3.0
|
15.4
|
0.5
|
C4D
|
A:HEM501
|
3.0
|
15.4
|
0.5
|
C4A
|
A:HEM501
|
3.0
|
15.2
|
0.5
|
C1B
|
A:HEM501
|
3.0
|
16.0
|
0.5
|
C4C
|
A:HEM501
|
3.0
|
17.1
|
0.5
|
C1D
|
A:HEM501
|
3.0
|
15.5
|
0.5
|
C1A
|
A:HEM501
|
3.0
|
14.9
|
0.5
|
C4B
|
A:HEM501
|
3.0
|
16.6
|
0.5
|
C1B
|
A:HEM501
|
3.0
|
16.1
|
0.5
|
C1A
|
A:HEM501
|
3.0
|
15.6
|
0.5
|
C4B
|
A:HEM501
|
3.0
|
15.7
|
0.5
|
C4C
|
A:HEM501
|
3.1
|
16.2
|
0.5
|
C4A
|
A:HEM501
|
3.1
|
15.3
|
0.5
|
C1C
|
A:HEM501
|
3.1
|
16.6
|
0.5
|
C1C
|
A:HEM501
|
3.1
|
16.2
|
0.5
|
CHD
|
A:HEM501
|
3.3
|
17.1
|
0.5
|
CHB
|
A:HEM501
|
3.4
|
16.2
|
0.5
|
CA
|
A:NEH503
|
3.4
|
31.1
|
1.0
|
CHA
|
A:HEM501
|
3.4
|
15.4
|
0.5
|
CHA
|
A:HEM501
|
3.4
|
15.1
|
0.5
|
CHD
|
A:HEM501
|
3.4
|
16.2
|
0.5
|
CHC
|
A:HEM501
|
3.4
|
16.6
|
0.5
|
CB
|
A:CYS400
|
3.4
|
14.3
|
1.0
|
CHB
|
A:HEM501
|
3.5
|
16.0
|
0.5
|
CHC
|
A:HEM501
|
3.5
|
15.8
|
0.5
|
CA
|
A:CYS400
|
4.1
|
15.2
|
1.0
|
C2D
|
A:HEM501
|
4.2
|
16.3
|
0.5
|
C3A
|
A:HEM501
|
4.2
|
15.7
|
0.5
|
C3D
|
A:HEM501
|
4.2
|
15.5
|
0.5
|
C2A
|
A:HEM501
|
4.2
|
14.9
|
0.5
|
C3C
|
A:HEM501
|
4.3
|
18.1
|
0.5
|
C2B
|
A:HEM501
|
4.3
|
15.8
|
0.5
|
C2B
|
A:HEM501
|
4.3
|
16.5
|
0.5
|
C2D
|
A:HEM501
|
4.3
|
16.1
|
0.5
|
C2C
|
A:HEM501
|
4.3
|
17.3
|
0.5
|
C3B
|
A:HEM501
|
4.3
|
16.4
|
0.5
|
C3D
|
A:HEM501
|
4.3
|
15.9
|
0.5
|
C2A
|
A:HEM501
|
4.3
|
15.9
|
0.5
|
C3C
|
A:HEM501
|
4.3
|
17.0
|
0.5
|
C3A
|
A:HEM501
|
4.3
|
16.1
|
0.5
|
C2C
|
A:HEM501
|
4.3
|
16.4
|
0.5
|
C3B
|
A:HEM501
|
4.3
|
15.8
|
0.5
|
CB
|
A:NEH503
|
4.6
|
31.1
|
1.0
|
N
|
A:GLY402
|
4.8
|
17.2
|
1.0
|
C
|
A:CYS400
|
4.9
|
15.4
|
1.0
|
CB
|
A:ALA264
|
5.0
|
22.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 7d0u
Go back to
Iron Binding Sites List in 7d0u
Iron binding site 2 out
of 4 in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine
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 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:16.4
occ:0.50
|
FE
|
A:HEM501
|
0.0
|
16.4
|
0.5
|
FE
|
A:HEM501
|
0.1
|
16.4
|
0.5
|
ND
|
A:HEM501
|
1.9
|
16.4
|
0.5
|
ND
|
A:HEM501
|
2.0
|
15.7
|
0.5
|
NA
|
A:HEM501
|
2.0
|
16.5
|
0.5
|
NB
|
A:HEM501
|
2.0
|
15.4
|
0.5
|
NA
|
A:HEM501
|
2.0
|
15.3
|
0.5
|
NC
|
A:HEM501
|
2.0
|
15.2
|
0.5
|
NB
|
A:HEM501
|
2.1
|
16.0
|
0.5
|
NC
|
A:HEM501
|
2.1
|
16.8
|
0.5
|
N
|
A:NEH503
|
2.3
|
19.6
|
1.0
|
SG
|
A:CYS400
|
2.3
|
16.7
|
1.0
|
C1D
|
A:HEM501
|
2.9
|
15.5
|
0.5
|
C4D
|
A:HEM501
|
2.9
|
15.4
|
0.5
|
C1B
|
A:HEM501
|
3.0
|
16.1
|
0.5
|
C1D
|
A:HEM501
|
3.0
|
15.8
|
0.5
|
C4B
|
A:HEM501
|
3.0
|
16.6
|
0.5
|
C4D
|
A:HEM501
|
3.0
|
15.4
|
0.5
|
C4C
|
A:HEM501
|
3.0
|
16.2
|
0.5
|
C1A
|
A:HEM501
|
3.0
|
15.6
|
0.5
|
C4A
|
A:HEM501
|
3.0
|
15.3
|
0.5
|
C1A
|
A:HEM501
|
3.0
|
14.9
|
0.5
|
C4A
|
A:HEM501
|
3.0
|
15.2
|
0.5
|
C1B
|
A:HEM501
|
3.1
|
16.0
|
0.5
|
C4B
|
A:HEM501
|
3.1
|
15.7
|
0.5
|
C4C
|
A:HEM501
|
3.1
|
17.1
|
0.5
|
C1C
|
A:HEM501
|
3.1
|
16.2
|
0.5
|
C1C
|
A:HEM501
|
3.1
|
16.6
|
0.5
|
CHD
|
A:HEM501
|
3.3
|
16.2
|
0.5
|
CB
|
A:CYS400
|
3.4
|
14.3
|
1.0
|
CHB
|
A:HEM501
|
3.4
|
16.0
|
0.5
|
CHA
|
A:HEM501
|
3.4
|
15.4
|
0.5
|
CHA
|
A:HEM501
|
3.4
|
15.1
|
0.5
|
CHD
|
A:HEM501
|
3.4
|
17.1
|
0.5
|
CHB
|
A:HEM501
|
3.4
|
16.2
|
0.5
|
CHC
|
A:HEM501
|
3.4
|
16.6
|
0.5
|
CA
|
A:NEH503
|
3.5
|
31.1
|
1.0
|
CHC
|
A:HEM501
|
3.5
|
15.8
|
0.5
|
CA
|
A:CYS400
|
4.0
|
15.2
|
1.0
|
C2B
|
A:HEM501
|
4.2
|
16.5
|
0.5
|
C2D
|
A:HEM501
|
4.2
|
16.1
|
0.5
|
C3C
|
A:HEM501
|
4.2
|
17.0
|
0.5
|
C3A
|
A:HEM501
|
4.2
|
16.1
|
0.5
|
C3B
|
A:HEM501
|
4.2
|
16.4
|
0.5
|
C3D
|
A:HEM501
|
4.2
|
15.9
|
0.5
|
C2A
|
A:HEM501
|
4.2
|
15.9
|
0.5
|
C2D
|
A:HEM501
|
4.2
|
16.3
|
0.5
|
C2C
|
A:HEM501
|
4.2
|
16.4
|
0.5
|
C3A
|
A:HEM501
|
4.2
|
15.7
|
0.5
|
C3D
|
A:HEM501
|
4.2
|
15.5
|
0.5
|
C2A
|
A:HEM501
|
4.3
|
14.9
|
0.5
|
C3C
|
A:HEM501
|
4.3
|
18.1
|
0.5
|
C2C
|
A:HEM501
|
4.3
|
17.3
|
0.5
|
C2B
|
A:HEM501
|
4.3
|
15.8
|
0.5
|
C3B
|
A:HEM501
|
4.3
|
15.8
|
0.5
|
CB
|
A:NEH503
|
4.6
|
31.1
|
1.0
|
C
|
A:CYS400
|
4.8
|
15.4
|
1.0
|
N
|
A:GLY402
|
4.8
|
17.2
|
1.0
|
N
|
A:ILE401
|
5.0
|
16.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 7d0u
Go back to
Iron Binding Sites List in 7d0u
Iron binding site 3 out
of 4 in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine
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 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:17.6
occ:0.50
|
FE
|
B:HEM502
|
0.0
|
17.6
|
0.5
|
FE
|
B:HEM502
|
0.1
|
17.4
|
0.5
|
ND
|
B:HEM502
|
1.9
|
16.4
|
0.5
|
ND
|
B:HEM502
|
2.0
|
17.3
|
0.5
|
NA
|
B:HEM502
|
2.0
|
16.2
|
0.5
|
NA
|
B:HEM502
|
2.0
|
17.6
|
0.5
|
NB
|
B:HEM502
|
2.1
|
16.6
|
0.5
|
NC
|
B:HEM502
|
2.1
|
17.5
|
0.5
|
NB
|
B:HEM502
|
2.1
|
17.1
|
0.5
|
NC
|
B:HEM502
|
2.1
|
16.1
|
0.5
|
N
|
B:NEH504
|
2.1
|
21.3
|
0.6
|
N
|
B:NEH504
|
2.3
|
24.0
|
0.4
|
SG
|
B:CYS400
|
2.3
|
17.4
|
1.0
|
CA
|
B:NEH504
|
2.8
|
28.0
|
0.4
|
C1D
|
B:HEM502
|
2.9
|
16.9
|
0.5
|
C4D
|
B:HEM502
|
3.0
|
17.5
|
0.5
|
C1D
|
B:HEM502
|
3.0
|
16.8
|
0.5
|
C4D
|
B:HEM502
|
3.0
|
17.4
|
0.5
|
C4C
|
B:HEM502
|
3.0
|
17.8
|
0.5
|
C1A
|
B:HEM502
|
3.0
|
17.5
|
0.5
|
C4A
|
B:HEM502
|
3.0
|
16.6
|
0.5
|
C4C
|
B:HEM502
|
3.0
|
16.6
|
0.5
|
C1B
|
B:HEM502
|
3.0
|
16.6
|
0.5
|
C4B
|
B:HEM502
|
3.0
|
17.7
|
0.5
|
C1B
|
B:HEM502
|
3.0
|
17.2
|
0.5
|
C4B
|
B:HEM502
|
3.1
|
17.2
|
0.5
|
C1A
|
B:HEM502
|
3.1
|
17.5
|
0.5
|
C1C
|
B:HEM502
|
3.1
|
18.1
|
0.5
|
C4A
|
B:HEM502
|
3.1
|
16.9
|
0.5
|
C1C
|
B:HEM502
|
3.1
|
17.0
|
0.5
|
CA
|
B:NEH504
|
3.3
|
31.0
|
0.6
|
CHD
|
B:HEM502
|
3.4
|
18.3
|
0.5
|
CHD
|
B:HEM502
|
3.4
|
16.5
|
0.5
|
CHB
|
B:HEM502
|
3.4
|
17.2
|
0.5
|
CHA
|
B:HEM502
|
3.4
|
16.9
|
0.5
|
CHA
|
B:HEM502
|
3.4
|
16.7
|
0.5
|
CHC
|
B:HEM502
|
3.5
|
17.9
|
0.5
|
CHB
|
B:HEM502
|
3.5
|
17.0
|
0.5
|
CB
|
B:CYS400
|
3.5
|
15.9
|
1.0
|
CHC
|
B:HEM502
|
3.5
|
17.2
|
0.5
|
CB
|
B:NEH504
|
3.7
|
26.4
|
0.4
|
CA
|
B:CYS400
|
4.1
|
15.1
|
1.0
|
C2D
|
B:HEM502
|
4.2
|
17.6
|
0.5
|
C3A
|
B:HEM502
|
4.2
|
17.6
|
0.5
|
C3D
|
B:HEM502
|
4.2
|
16.9
|
0.5
|
C2A
|
B:HEM502
|
4.2
|
16.8
|
0.5
|
C3C
|
B:HEM502
|
4.2
|
18.4
|
0.5
|
CB
|
B:NEH504
|
4.2
|
30.3
|
0.6
|
C2C
|
B:HEM502
|
4.3
|
18.4
|
0.5
|
C2D
|
B:HEM502
|
4.3
|
17.1
|
0.5
|
C3C
|
B:HEM502
|
4.3
|
16.6
|
0.5
|
C2B
|
B:HEM502
|
4.3
|
16.8
|
0.5
|
C3D
|
B:HEM502
|
4.3
|
17.3
|
0.5
|
C2C
|
B:HEM502
|
4.3
|
16.3
|
0.5
|
C2A
|
B:HEM502
|
4.3
|
17.4
|
0.5
|
C3A
|
B:HEM502
|
4.3
|
17.3
|
0.5
|
C2B
|
B:HEM502
|
4.3
|
16.1
|
0.5
|
C3B
|
B:HEM502
|
4.3
|
17.6
|
0.5
|
C3B
|
B:HEM502
|
4.3
|
17.4
|
0.5
|
C
|
B:CYS400
|
4.9
|
16.0
|
1.0
|
N
|
B:GLY402
|
4.9
|
19.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 7d0u
Go back to
Iron Binding Sites List in 7d0u
Iron binding site 4 out
of 4 in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine
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 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Ethylamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:17.4
occ:0.50
|
FE
|
B:HEM502
|
0.0
|
17.4
|
0.5
|
FE
|
B:HEM502
|
0.1
|
17.6
|
0.5
|
ND
|
B:HEM502
|
1.9
|
17.3
|
0.5
|
ND
|
B:HEM502
|
2.0
|
16.4
|
0.5
|
NA
|
B:HEM502
|
2.0
|
17.6
|
0.5
|
NA
|
B:HEM502
|
2.0
|
16.2
|
0.5
|
NB
|
B:HEM502
|
2.0
|
17.1
|
0.5
|
NC
|
B:HEM502
|
2.0
|
16.1
|
0.5
|
NB
|
B:HEM502
|
2.1
|
16.6
|
0.5
|
NC
|
B:HEM502
|
2.1
|
17.5
|
0.5
|
N
|
B:NEH504
|
2.2
|
21.3
|
0.6
|
SG
|
B:CYS400
|
2.3
|
17.4
|
1.0
|
N
|
B:NEH504
|
2.3
|
24.0
|
0.4
|
CA
|
B:NEH504
|
2.9
|
28.0
|
0.4
|
C1D
|
B:HEM502
|
2.9
|
16.8
|
0.5
|
C4D
|
B:HEM502
|
3.0
|
17.4
|
0.5
|
C4D
|
B:HEM502
|
3.0
|
17.5
|
0.5
|
C4C
|
B:HEM502
|
3.0
|
16.6
|
0.5
|
C1D
|
B:HEM502
|
3.0
|
16.9
|
0.5
|
C1B
|
B:HEM502
|
3.0
|
17.2
|
0.5
|
C4B
|
B:HEM502
|
3.0
|
17.7
|
0.5
|
C1A
|
B:HEM502
|
3.0
|
17.5
|
0.5
|
C4A
|
B:HEM502
|
3.0
|
16.9
|
0.5
|
C1A
|
B:HEM502
|
3.0
|
17.5
|
0.5
|
C4C
|
B:HEM502
|
3.1
|
17.8
|
0.5
|
C1C
|
B:HEM502
|
3.1
|
17.0
|
0.5
|
C4B
|
B:HEM502
|
3.1
|
17.2
|
0.5
|
C4A
|
B:HEM502
|
3.1
|
16.6
|
0.5
|
C1B
|
B:HEM502
|
3.1
|
16.6
|
0.5
|
C1C
|
B:HEM502
|
3.1
|
18.1
|
0.5
|
CA
|
B:NEH504
|
3.3
|
31.0
|
0.6
|
CHD
|
B:HEM502
|
3.3
|
16.5
|
0.5
|
CB
|
B:CYS400
|
3.4
|
15.9
|
1.0
|
CHB
|
B:HEM502
|
3.4
|
17.0
|
0.5
|
CHA
|
B:HEM502
|
3.4
|
16.9
|
0.5
|
CHA
|
B:HEM502
|
3.4
|
16.7
|
0.5
|
CHD
|
B:HEM502
|
3.4
|
18.3
|
0.5
|
CHC
|
B:HEM502
|
3.5
|
17.9
|
0.5
|
CHC
|
B:HEM502
|
3.5
|
17.2
|
0.5
|
CHB
|
B:HEM502
|
3.5
|
17.2
|
0.5
|
CB
|
B:NEH504
|
3.8
|
26.4
|
0.4
|
CA
|
B:CYS400
|
4.0
|
15.1
|
1.0
|
C2D
|
B:HEM502
|
4.2
|
17.1
|
0.5
|
C3C
|
B:HEM502
|
4.2
|
16.6
|
0.5
|
C2B
|
B:HEM502
|
4.2
|
16.8
|
0.5
|
C3A
|
B:HEM502
|
4.2
|
17.3
|
0.5
|
C2D
|
B:HEM502
|
4.2
|
17.6
|
0.5
|
C3D
|
B:HEM502
|
4.2
|
17.3
|
0.5
|
C2A
|
B:HEM502
|
4.2
|
17.4
|
0.5
|
C2C
|
B:HEM502
|
4.2
|
16.3
|
0.5
|
C3D
|
B:HEM502
|
4.3
|
16.9
|
0.5
|
C2A
|
B:HEM502
|
4.3
|
16.8
|
0.5
|
C3A
|
B:HEM502
|
4.3
|
17.6
|
0.5
|
C3B
|
B:HEM502
|
4.3
|
17.6
|
0.5
|
C3C
|
B:HEM502
|
4.3
|
18.4
|
0.5
|
C2C
|
B:HEM502
|
4.3
|
18.4
|
0.5
|
CB
|
B:NEH504
|
4.3
|
30.3
|
0.6
|
C2B
|
B:HEM502
|
4.4
|
16.1
|
0.5
|
C3B
|
B:HEM502
|
4.4
|
17.4
|
0.5
|
C
|
B:CYS400
|
4.8
|
16.0
|
1.0
|
N
|
B:GLY402
|
4.9
|
19.5
|
1.0
|
N
|
B:ILE401
|
5.0
|
16.8
|
1.0
|
|
Reference:
O.Shoji,
J.K.Stanfield.
Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L-Phenylalanine in Complex with Ethylamine at 1.68 Angstrom Resolution To Be Published.
Page generated: Thu Aug 8 03:33:02 2024
|