Iron in PDB 5xa3: Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine
Enzymatic activity of Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine
All present enzymatic activity of Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine:
1.14.14.1;
1.6.2.4;
Protein crystallography data
The structure of Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine, PDB code: 5xa3
was solved by
O.Shoji,
S.Yanagisawa,
J.K.Stanfield,
K.Suzuki,
C.Kasai,
Z.Cong,
H.Sugimoto,
Y.Shiro,
Y.Watanabe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.234,
58.522,
145.952,
90.00,
90.02,
90.00
|
R / Rfree (%)
|
22.1 /
25.3
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine
(pdb code 5xa3). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine, PDB code: 5xa3:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5xa3
Go back to
Iron Binding Sites List in 5xa3
Iron binding site 1 out
of 4 in the Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:10.0
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
10.0
|
1.0
|
ND
|
A:HEM501
|
1.9
|
10.0
|
1.0
|
NA
|
A:HEM501
|
2.0
|
10.0
|
1.0
|
NC
|
A:HEM501
|
2.1
|
10.1
|
1.0
|
NB
|
A:HEM501
|
2.1
|
10.1
|
1.0
|
SG
|
A:CYS400
|
2.4
|
10.2
|
1.0
|
S
|
A:DMS502
|
2.8
|
36.9
|
1.0
|
C4D
|
A:HEM501
|
2.9
|
9.9
|
1.0
|
C1D
|
A:HEM501
|
2.9
|
10.0
|
1.0
|
C1A
|
A:HEM501
|
3.0
|
9.9
|
1.0
|
C4A
|
A:HEM501
|
3.0
|
10.0
|
1.0
|
C4B
|
A:HEM501
|
3.1
|
10.1
|
1.0
|
C1B
|
A:HEM501
|
3.1
|
10.1
|
1.0
|
C4C
|
A:HEM501
|
3.1
|
10.1
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
10.1
|
1.0
|
C1
|
A:DMS502
|
3.2
|
36.6
|
1.0
|
CHA
|
A:HEM501
|
3.4
|
9.9
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
10.0
|
1.0
|
CB
|
A:CYS400
|
3.4
|
10.2
|
1.0
|
CHB
|
A:HEM501
|
3.4
|
10.0
|
1.0
|
CHC
|
A:HEM501
|
3.5
|
10.1
|
1.0
|
C2
|
A:DMS502
|
3.9
|
36.8
|
1.0
|
O
|
A:DMS502
|
3.9
|
38.5
|
1.0
|
CA
|
A:CYS400
|
4.1
|
10.2
|
1.0
|
C3D
|
A:HEM501
|
4.2
|
9.9
|
1.0
|
C2D
|
A:HEM501
|
4.2
|
9.9
|
1.0
|
C2A
|
A:HEM501
|
4.2
|
9.9
|
1.0
|
C3A
|
A:HEM501
|
4.2
|
9.9
|
1.0
|
C3C
|
A:HEM501
|
4.3
|
10.2
|
1.0
|
C2B
|
A:HEM501
|
4.3
|
10.1
|
1.0
|
C2C
|
A:HEM501
|
4.3
|
10.2
|
1.0
|
C3B
|
A:HEM501
|
4.3
|
10.2
|
1.0
|
N
|
A:GLY402
|
4.9
|
10.8
|
1.0
|
C
|
A:CYS400
|
4.9
|
10.3
|
1.0
|
CB
|
A:ALA264
|
5.0
|
21.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 5xa3
Go back to
Iron Binding Sites List in 5xa3
Iron binding site 2 out
of 4 in the Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:8.8
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
8.8
|
1.0
|
ND
|
B:HEM501
|
1.9
|
8.8
|
1.0
|
NA
|
B:HEM501
|
2.0
|
8.8
|
1.0
|
NC
|
B:HEM501
|
2.1
|
8.8
|
1.0
|
NB
|
B:HEM501
|
2.1
|
8.8
|
1.0
|
SG
|
B:CYS400
|
2.4
|
8.6
|
1.0
|
O
|
B:DMS502
|
2.7
|
26.3
|
1.0
|
S
|
B:DMS502
|
2.8
|
26.2
|
1.0
|
C1D
|
B:HEM501
|
2.9
|
8.8
|
1.0
|
C4D
|
B:HEM501
|
2.9
|
8.8
|
1.0
|
C1A
|
B:HEM501
|
3.0
|
8.8
|
1.0
|
C4A
|
B:HEM501
|
3.0
|
8.8
|
1.0
|
C4B
|
B:HEM501
|
3.1
|
8.9
|
1.0
|
C1B
|
B:HEM501
|
3.1
|
8.9
|
1.0
|
C4C
|
B:HEM501
|
3.1
|
8.9
|
1.0
|
C1C
|
B:HEM501
|
3.1
|
8.9
|
1.0
|
CHA
|
B:HEM501
|
3.4
|
8.8
|
1.0
|
CHD
|
B:HEM501
|
3.4
|
8.8
|
1.0
|
CB
|
B:CYS400
|
3.4
|
8.7
|
1.0
|
CHB
|
B:HEM501
|
3.4
|
8.9
|
1.0
|
CHC
|
B:HEM501
|
3.5
|
8.9
|
1.0
|
C1
|
B:DMS502
|
4.0
|
26.3
|
1.0
|
CA
|
B:CYS400
|
4.1
|
8.7
|
1.0
|
C2
|
B:DMS502
|
4.1
|
26.3
|
1.0
|
C3D
|
B:HEM501
|
4.2
|
8.8
|
1.0
|
C2D
|
B:HEM501
|
4.2
|
8.8
|
1.0
|
C2A
|
B:HEM501
|
4.2
|
8.8
|
1.0
|
C3A
|
B:HEM501
|
4.2
|
8.8
|
1.0
|
C2B
|
B:HEM501
|
4.3
|
8.9
|
1.0
|
C3C
|
B:HEM501
|
4.3
|
8.9
|
1.0
|
C2C
|
B:HEM501
|
4.3
|
8.9
|
1.0
|
C3B
|
B:HEM501
|
4.3
|
8.9
|
1.0
|
CB
|
B:ALA264
|
4.8
|
19.6
|
1.0
|
C
|
B:CYS400
|
4.9
|
8.8
|
1.0
|
N
|
B:GLY402
|
4.9
|
9.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 5xa3
Go back to
Iron Binding Sites List in 5xa3
Iron binding site 3 out
of 4 in the Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:9.7
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
9.7
|
1.0
|
ND
|
C:HEM501
|
1.9
|
9.6
|
1.0
|
NA
|
C:HEM501
|
2.0
|
9.7
|
1.0
|
NC
|
C:HEM501
|
2.1
|
9.7
|
1.0
|
NB
|
C:HEM501
|
2.1
|
9.7
|
1.0
|
SG
|
C:CYS400
|
2.4
|
8.5
|
1.0
|
S
|
C:DMS502
|
2.9
|
31.2
|
1.0
|
C4D
|
C:HEM501
|
2.9
|
9.6
|
1.0
|
C1D
|
C:HEM501
|
2.9
|
9.6
|
1.0
|
C1A
|
C:HEM501
|
3.0
|
9.7
|
1.0
|
C4A
|
C:HEM501
|
3.0
|
9.7
|
1.0
|
C4B
|
C:HEM501
|
3.1
|
9.8
|
1.0
|
C1B
|
C:HEM501
|
3.1
|
9.8
|
1.0
|
C4C
|
C:HEM501
|
3.1
|
9.7
|
1.0
|
C2
|
C:DMS502
|
3.1
|
31.0
|
1.0
|
C1C
|
C:HEM501
|
3.1
|
9.7
|
1.0
|
CHA
|
C:HEM501
|
3.4
|
9.6
|
1.0
|
CB
|
C:CYS400
|
3.4
|
8.6
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
9.6
|
1.0
|
CHB
|
C:HEM501
|
3.4
|
9.8
|
1.0
|
CHC
|
C:HEM501
|
3.5
|
9.8
|
1.0
|
O
|
C:DMS502
|
3.9
|
32.1
|
1.0
|
C1
|
C:DMS502
|
4.0
|
31.5
|
1.0
|
CA
|
C:CYS400
|
4.1
|
8.6
|
1.0
|
C3D
|
C:HEM501
|
4.2
|
9.6
|
1.0
|
C2D
|
C:HEM501
|
4.2
|
9.6
|
1.0
|
C2A
|
C:HEM501
|
4.2
|
9.7
|
1.0
|
C3A
|
C:HEM501
|
4.2
|
9.7
|
1.0
|
C3C
|
C:HEM501
|
4.3
|
9.8
|
1.0
|
C2B
|
C:HEM501
|
4.3
|
9.8
|
1.0
|
C2C
|
C:HEM501
|
4.3
|
9.8
|
1.0
|
C3B
|
C:HEM501
|
4.3
|
9.8
|
1.0
|
C
|
C:CYS400
|
4.9
|
8.6
|
1.0
|
CB
|
C:ALA264
|
4.9
|
18.9
|
1.0
|
N
|
C:GLY402
|
5.0
|
9.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 5xa3
Go back to
Iron Binding Sites List in 5xa3
Iron binding site 4 out
of 4 in the Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-Prolyl-L- Phenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:10.6
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
10.6
|
1.0
|
ND
|
D:HEM501
|
1.9
|
10.6
|
1.0
|
NA
|
D:HEM501
|
2.0
|
10.6
|
1.0
|
NC
|
D:HEM501
|
2.1
|
10.7
|
1.0
|
NB
|
D:HEM501
|
2.1
|
10.7
|
1.0
|
SG
|
D:CYS400
|
2.4
|
10.8
|
1.0
|
S
|
D:DMS502
|
2.8
|
33.2
|
1.0
|
C4D
|
D:HEM501
|
2.9
|
10.6
|
1.0
|
C1D
|
D:HEM501
|
2.9
|
10.6
|
1.0
|
C1A
|
D:HEM501
|
3.0
|
10.5
|
1.0
|
C4A
|
D:HEM501
|
3.0
|
10.6
|
1.0
|
C4B
|
D:HEM501
|
3.1
|
10.7
|
1.0
|
C1B
|
D:HEM501
|
3.1
|
10.7
|
1.0
|
C4C
|
D:HEM501
|
3.1
|
10.7
|
1.0
|
C1C
|
D:HEM501
|
3.1
|
10.7
|
1.0
|
C2
|
D:DMS502
|
3.2
|
32.9
|
1.0
|
CHA
|
D:HEM501
|
3.4
|
10.5
|
1.0
|
CHD
|
D:HEM501
|
3.4
|
10.6
|
1.0
|
CB
|
D:CYS400
|
3.4
|
10.7
|
1.0
|
CHB
|
D:HEM501
|
3.4
|
10.7
|
1.0
|
CHC
|
D:HEM501
|
3.5
|
10.7
|
1.0
|
O
|
D:DMS502
|
3.5
|
33.8
|
1.0
|
CA
|
D:CYS400
|
4.1
|
10.7
|
1.0
|
C3D
|
D:HEM501
|
4.2
|
10.6
|
1.0
|
C1
|
D:DMS502
|
4.2
|
33.5
|
1.0
|
C2D
|
D:HEM501
|
4.2
|
10.6
|
1.0
|
C2A
|
D:HEM501
|
4.2
|
10.5
|
1.0
|
C3A
|
D:HEM501
|
4.2
|
10.5
|
1.0
|
C3C
|
D:HEM501
|
4.3
|
10.7
|
1.0
|
C2B
|
D:HEM501
|
4.3
|
10.7
|
1.0
|
C2C
|
D:HEM501
|
4.3
|
10.7
|
1.0
|
C3B
|
D:HEM501
|
4.3
|
10.8
|
1.0
|
N
|
D:GLY402
|
4.9
|
11.4
|
1.0
|
C
|
D:CYS400
|
4.9
|
10.8
|
1.0
|
CB
|
D:ALA264
|
4.9
|
21.3
|
1.0
|
|
Reference:
O.Shoji,
S.Yanagisawa,
J.K.Stanfield,
K.Suzuki,
Z.Cong,
H.Sugimoto,
Y.Shiro,
Y.Watanabe.
Direct Hydroxylation of Benzene to Phenol By Cytochrome P450BM3 Triggered By Amino Acid Derivatives. Angew. Chem. Int. Ed. Engl. V. 56 10324 2017.
ISSN: ESSN 1521-3773
PubMed: 28544674
DOI: 10.1002/ANIE.201703461
Page generated: Tue Aug 6 11:32:40 2024
|