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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: Wed Aug 6 02:43:14 2025

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