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Iron in PDB 9kt5: Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose

Enzymatic activity of Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose

All present enzymatic activity of Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose:
1.14.14.1; 1.6.2.4;

Protein crystallography data

The structure of Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose, PDB code: 9kt5 was solved by S.Nagao, W.Kuwano, T.Tosha, K.Yamashita, J.K.Stanfield, C.Kasai, S.Ariyasu, O.Shoji, H.Sugimoto, M.Kubo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.64 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.13, 129.34, 150.15, 90, 90, 90
R / Rfree (%) 14.9 / 20

Iron Binding Sites:

The binding sites of Iron atom in the Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose (pdb code 9kt5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose, PDB code: 9kt5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 9kt5

Go back to Iron Binding Sites List in 9kt5
Iron binding site 1 out of 4 in the Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:11.8
occ:0.50
 FE A:HEM501 0.0 11.8 0.5
FE A:HEM501 0.1 13.4 0.5
O1 A:OXY503 2.0 11.1 0.5
NB A:HEM501 2.1 12.0 1.0
NC A:HEM501 2.1 11.8 1.0
ND A:HEM501 2.1 11.4 1.0
NA A:HEM501 2.1 11.4 1.0
SG A:CYS400 2.4 13.2 1.0
O2 A:OXY503 2.8 14.5 0.5
C4C A:HEM501 3.0 11.7 1.0
C4B A:HEM501 3.0 12.1 1.0
C1B A:HEM501 3.0 11.1 1.0
C4D A:HEM501 3.0 9.9 1.0
C1D A:HEM501 3.0 10.6 1.0
C1A A:HEM501 3.1 10.2 1.0
C1C A:HEM501 3.1 12.5 1.0
C4A A:HEM501 3.1 10.3 1.0
CB A:CYS400 3.4 12.1 1.0
CHD A:HEM501 3.4 11.6 1.0
CHA A:HEM501 3.5 10.0 1.0
CHC A:HEM501 3.5 12.9 1.0
CHB A:HEM501 3.5 12.2 1.0
O A:HOH608 3.5 13.3 0.2
CA A:CYS400 4.2 10.1 1.0
C3C A:HEM501 4.2 13.4 1.0
C2B A:HEM501 4.3 9.8 1.0
C2C A:HEM501 4.3 14.2 1.0
C2A A:HEM501 4.3 10.2 1.0
C3B A:HEM501 4.3 12.1 1.0
O A:HOH852 4.3 18.7 0.4
C3D A:HEM501 4.3 10.4 1.0
C2D A:HEM501 4.3 11.3 1.0
C3A A:HEM501 4.3 9.5 1.0
CAA A:SYN502 4.6 20.0 0.7
O A:ALA264 4.7 16.9 1.0
CD2 A:HIS393 4.8 15.4 0.6
CB A:ALA264 4.9 15.9 1.0
C A:CYS400 4.9 11.8 1.0
N A:GLY402 5.0 11.1 1.0
OG1 A:THR268 5.0 16.5 1.0

Iron binding site 2 out of 4 in 9kt5

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Iron binding site 2 out of 4 in the Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:13.4
occ:0.50
 FE A:HEM501 0.0 13.4 0.5
FE A:HEM501 0.1 11.8 0.5
ND A:HEM501 2.0 11.4 1.0
NC A:HEM501 2.1 11.8 1.0
NA A:HEM501 2.1 11.4 1.0
NB A:HEM501 2.1 12.0 1.0
O1 A:OXY503 2.1 11.1 0.5
SG A:CYS400 2.4 13.2 1.0
O2 A:OXY503 2.9 14.5 0.5
C4C A:HEM501 3.0 11.7 1.0
C4D A:HEM501 3.0 9.9 1.0
C1D A:HEM501 3.0 10.6 1.0
C1A A:HEM501 3.0 10.2 1.0
C4B A:HEM501 3.1 12.1 1.0
C1B A:HEM501 3.1 11.1 1.0
C1C A:HEM501 3.1 12.5 1.0
C4A A:HEM501 3.1 10.3 1.0
CB A:CYS400 3.3 12.1 1.0
CHD A:HEM501 3.4 11.6 1.0
CHA A:HEM501 3.4 10.0 1.0
CHC A:HEM501 3.5 12.9 1.0
CHB A:HEM501 3.5 12.2 1.0
O A:HOH608 3.6 13.3 0.2
CA A:CYS400 4.1 10.1 1.0
C3C A:HEM501 4.2 13.4 1.0
C2A A:HEM501 4.3 10.2 1.0
C3D A:HEM501 4.3 10.4 1.0
O A:HOH852 4.3 18.7 0.4
C2C A:HEM501 4.3 14.2 1.0
C2D A:HEM501 4.3 11.3 1.0
C2B A:HEM501 4.3 9.8 1.0
C3A A:HEM501 4.3 9.5 1.0
C3B A:HEM501 4.3 12.1 1.0
CAA A:SYN502 4.6 20.0 0.7
O A:ALA264 4.8 16.9 1.0
CD2 A:HIS393 4.8 15.4 0.6
C A:CYS400 4.9 11.8 1.0
N A:GLY402 4.9 11.1 1.0
CB A:ALA264 5.0 15.9 1.0

Iron binding site 3 out of 4 in 9kt5

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Iron binding site 3 out of 4 in the Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.8
occ:0.50
 FE B:HEM501 0.0 11.8 0.5
FE B:HEM501 0.1 13.2 0.5
NC B:HEM501 2.0 11.1 1.0
NB B:HEM501 2.1 11.1 1.0
NA B:HEM501 2.1 12.1 1.0
ND B:HEM501 2.1 11.0 1.0
O1 B:OXY503 2.1 10.7 0.5
SG B:CYS400 2.4 12.9 1.0
O2 B:OXY503 3.0 13.7 0.5
C4C B:HEM501 3.0 11.3 1.0
C4B B:HEM501 3.0 10.7 1.0
C1B B:HEM501 3.0 12.2 1.0
C4D B:HEM501 3.0 11.3 1.0
C1D B:HEM501 3.1 12.1 1.0
C1A B:HEM501 3.1 10.1 1.0
C1C B:HEM501 3.1 10.9 1.0
C4A B:HEM501 3.1 12.6 1.0
CB B:CYS400 3.4 10.7 1.0
O B:HOH602 3.4 14.6 0.2
CHD B:HEM501 3.4 11.1 1.0
CHA B:HEM501 3.5 11.3 1.0
CHC B:HEM501 3.5 12.9 1.0
CHB B:HEM501 3.5 10.8 1.0
CA B:CYS400 4.1 9.9 1.0
C3C B:HEM501 4.2 12.6 1.0
C2C B:HEM501 4.3 11.8 1.0
C2B B:HEM501 4.3 11.1 1.0
C3B B:HEM501 4.3 10.4 1.0
C2A B:HEM501 4.3 9.5 1.0
O B:HOH937 4.3 14.9 0.2
C3A B:HEM501 4.3 10.1 1.0
C3D B:HEM501 4.3 12.8 1.0
C2D B:HEM501 4.3 11.4 1.0
CAA B:SYN502 4.5 18.8 0.7
O B:ALA264 4.7 17.6 1.0
CB B:ALA264 4.8 16.5 1.0
CD2 B:HIS393 4.9 18.1 0.8
C B:CYS400 4.9 10.2 1.0
N B:GLY402 5.0 12.3 1.0
OG1 B:THR268 5.0 13.9 1.0
N B:ILE401 5.0 11.1 1.0

Iron binding site 4 out of 4 in 9kt5

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Iron binding site 4 out of 4 in the Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Synchrotron X-Ray Crystal Structure of Oxygen-Bound F87A/F393H P450BM3 with Decoy C7PROPHE (N-Enanthyl-L-Prolyl-L-Phenylalanine) and Substrate Styrene at 2 Mgy X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:13.2
occ:0.50
 FE B:HEM501 0.0 13.2 0.5
FE B:HEM501 0.1 11.8 0.5
ND B:HEM501 2.1 11.0 1.0
NC B:HEM501 2.1 11.1 1.0
NA B:HEM501 2.1 12.1 1.0
NB B:HEM501 2.1 11.1 1.0
O1 B:OXY503 2.1 10.7 0.5
SG B:CYS400 2.4 12.9 1.0
C4C B:HEM501 3.0 11.3 1.0
C4D B:HEM501 3.0 11.3 1.0
O2 B:OXY503 3.0 13.7 0.5
C1D B:HEM501 3.0 12.1 1.0
C4B B:HEM501 3.0 10.7 1.0
C1A B:HEM501 3.0 10.1 1.0
C1B B:HEM501 3.1 12.2 1.0
C1C B:HEM501 3.1 10.9 1.0
C4A B:HEM501 3.1 12.6 1.0
CB B:CYS400 3.3 10.7 1.0
CHD B:HEM501 3.4 11.1 1.0
CHA B:HEM501 3.4 11.3 1.0
O B:HOH602 3.5 14.6 0.2
CHC B:HEM501 3.5 12.9 1.0
CHB B:HEM501 3.5 10.8 1.0
CA B:CYS400 4.1 9.9 1.0
C3C B:HEM501 4.2 12.6 1.0
O B:HOH937 4.3 14.9 0.2
C2A B:HEM501 4.3 9.5 1.0
C2C B:HEM501 4.3 11.8 1.0
C3D B:HEM501 4.3 12.8 1.0
C2B B:HEM501 4.3 11.1 1.0
C2D B:HEM501 4.3 11.4 1.0
C3A B:HEM501 4.3 10.1 1.0
C3B B:HEM501 4.3 10.4 1.0
CAA B:SYN502 4.5 18.8 0.7
O B:ALA264 4.7 17.6 1.0
C B:CYS400 4.8 10.2 1.0
CD2 B:HIS393 4.8 18.1 0.8
CB B:ALA264 4.9 16.5 1.0
N B:GLY402 4.9 12.3 1.0
N B:ILE401 4.9 11.1 1.0

Reference:

S.Nagao, W.Kuwano, T.Tosha, K.Yamashita, J.K.Stanfield, C.Kasai, S.Ariyasu, K.Hirata, G.Ueno, H.Murakami, H.Ago, M.Yamamoto, O.Shoji, H.Sugimoto, M.Kubo. Xfel Crystallography Reveals Catalytic Cycle Dynamics During Non-Native Substrate Oxidation By Cytochrome P450BM3. Commun Chem V. 8 63 2025.
ISSN: ESSN 2399-3669
PubMed: 40075209
DOI: 10.1038/S42004-025-01440-2
Page generated: Fri Aug 8 07:06:38 2025

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