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Iron in PDB 8yaz: Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 with N-Enanthyl-L-Prolyl-L-Phenylalanine in Complex with Styrene

Enzymatic activity of Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 with N-Enanthyl-L-Prolyl-L-Phenylalanine in Complex with Styrene

All present enzymatic activity of Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 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 Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 with N-Enanthyl-L-Prolyl-L-Phenylalanine in Complex with Styrene, PDB code: 8yaz 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) 9.98 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.9, 128.44, 149.05, 90, 90, 90
R / Rfree (%) 18.6 / 22

Iron Binding Sites:

The binding sites of Iron atom in the Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 with N-Enanthyl-L-Prolyl-L-Phenylalanine in Complex with Styrene (pdb code 8yaz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 with N-Enanthyl-L-Prolyl-L-Phenylalanine in Complex with Styrene, PDB code: 8yaz:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 8yaz

Go back to Iron Binding Sites List in 8yaz
Iron binding site 1 out of 2 in the Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 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 Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 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:30.8
occ:1.00
 FE A:HEM501 0.0 30.8 1.0
ND A:HEM501 1.9 28.4 1.0
NA A:HEM501 2.0 29.7 1.0
NB A:HEM501 2.1 31.0 1.0
NC A:HEM501 2.1 32.4 1.0
O A:HOH714 2.1 33.4 0.5
SG A:CYS400 2.2 32.3 1.0
C1D A:HEM501 2.9 30.7 1.0
C4D A:HEM501 2.9 29.4 1.0
C1A A:HEM501 3.0 30.1 1.0
C4C A:HEM501 3.1 30.4 1.0
C1B A:HEM501 3.1 33.3 1.0
C4B A:HEM501 3.1 32.8 1.0
C4A A:HEM501 3.1 31.3 1.0
C1C A:HEM501 3.1 31.8 1.0
CB A:CYS400 3.2 27.8 1.0
CHD A:HEM501 3.4 30.8 1.0
CHA A:HEM501 3.4 33.0 1.0
CHB A:HEM501 3.5 32.6 1.0
CHC A:HEM501 3.5 30.8 1.0
CAD A:SYN503 3.8 38.8 0.7
CA A:CYS400 3.9 28.8 1.0
C2D A:HEM501 4.2 33.8 1.0
CAC A:SYN503 4.2 38.5 0.7
C3D A:HEM501 4.2 29.9 1.0
C2A A:HEM501 4.2 32.1 1.0
C3A A:HEM501 4.3 28.3 1.0
C3C A:HEM501 4.3 32.9 1.0
C2B A:HEM501 4.3 29.8 1.0
C2C A:HEM501 4.3 31.7 1.0
C3B A:HEM501 4.3 30.2 1.0
C A:CYS400 4.7 33.6 1.0
N A:GLY402 4.8 32.7 1.0
CAF A:SYN503 4.9 39.7 0.7
N A:ILE401 5.0 33.6 1.0

Iron binding site 2 out of 2 in 8yaz

Go back to Iron Binding Sites List in 8yaz
Iron binding site 2 out of 2 in the Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 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 Xfel Crystal Structure of the Oxidized Form of F87A/F393H P450BM3 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:31.0
occ:1.00
 FE B:HEM501 0.0 31.0 1.0
ND B:HEM501 1.9 27.5 1.0
NA B:HEM501 2.0 30.9 1.0
NC B:HEM501 2.1 31.5 1.0
NB B:HEM501 2.1 29.9 1.0
O B:HOH754 2.1 32.5 0.6
SG B:CYS400 2.2 32.5 1.0
C1D B:HEM501 2.9 31.0 1.0
C4D B:HEM501 2.9 32.3 1.0
C1A B:HEM501 3.0 31.6 1.0
C4B B:HEM501 3.0 31.6 1.0
C1B B:HEM501 3.0 29.0 1.0
C4C B:HEM501 3.1 33.2 1.0
C4A B:HEM501 3.1 30.7 1.0
C1C B:HEM501 3.1 35.0 1.0
CB B:CYS400 3.2 30.0 1.0
CHA B:HEM501 3.4 32.7 1.0
CHD B:HEM501 3.4 31.0 1.0
CHB B:HEM501 3.4 30.7 1.0
CHC B:HEM501 3.5 32.5 1.0
CAD B:SYN503 3.7 40.4 0.7
CA B:CYS400 4.0 28.6 1.0
C2D B:HEM501 4.2 31.9 1.0
C3D B:HEM501 4.2 29.8 1.0
C2A B:HEM501 4.2 30.6 1.0
C3A B:HEM501 4.2 30.5 1.0
C2B B:HEM501 4.3 27.5 1.0
C3C B:HEM501 4.3 32.4 1.0
C3B B:HEM501 4.3 29.9 1.0
C2C B:HEM501 4.3 34.5 1.0
CAF B:SYN503 4.5 42.8 0.7
CAC B:SYN503 4.6 35.5 0.7
C B:CYS400 4.7 30.9 1.0
N B:GLY402 4.8 35.7 1.0
CB B:ALA264 4.9 41.0 1.0
N B:ILE401 5.0 31.1 1.0
ND1 B:HIS393 5.0 38.2 1.0

Reference:

S.Nagao, W.Kuwano, T.Tosha, K.Yamashita, J.K.Stanfield, C.Kasai, S.Ariyasu, O.Shoji, H.Sugimoto, M.Kubo. Xfel Crystallography Reveals Dynamic Control of Non-Natural Substrate Binding in Cytochrome P450BM3 Catalytic Cycle To Be Published.
Page generated: Tue Feb 25 09:56:46 2025

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