Iron in PDB 7dvo: Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel

All present enzymatic activity of Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel:
1.7.1.14;

The structure of Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel, PDB code: 7dvo was solved by T.Nomura, T.Kimura, Y.Kanematsu, K.Yamashita, K.Hirata, G.Ueno, H.Murakami, T.Hisano, R.Yamagiwa, H.Takeda, C.Gopalasingam, K.Yuki, R.Kousaka, S.Yanagasawa, O.Shoji, T.Kumasaka, Y.Takano, H.Ago, M.Yamamoto, H.Sugimoto, T.Tosha, M.Kubo, Y.Shiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.27, 101.61, 73.19, 90, 92.71, 90
R / Rfree (%)	17.3 / 21.9

The binding sites of Iron atom in the Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel (pdb code 7dvo). 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 Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel, PDB code: 7dvo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:18.5 occ:0.40 FE A:HEM501 0.0 18.5 0.4 FE A:HEM501 0.0 18.4 0.6 N A:NO502 1.9 16.3 0.4 ND A:HEM501 1.9 19.3 0.6 ND A:HEM501 2.0 19.3 0.4 NA A:HEM501 2.0 17.9 0.6 NA A:HEM501 2.0 17.9 0.4 O A:HOH712 2.0 14.9 0.5 NB A:HEM501 2.0 17.6 0.6 NB A:HEM501 2.1 17.6 0.4 NC A:HEM501 2.1 20.0 0.4 NC A:HEM501 2.1 20.1 0.6 SG A:CYS352 2.3 18.6 0.4 SG A:CYS352 2.3 18.6 0.6 C1D A:HEM501 3.0 15.6 1.0 O A:NO502 3.0 20.4 0.4 C4D A:HEM501 3.0 19.2 1.0 C1A A:HEM501 3.0 18.4 1.0 C4A A:HEM501 3.0 16.4 1.0 C4C A:HEM501 3.1 19.8 1.0 C4B A:HEM501 3.1 16.4 1.0 C1B A:HEM501 3.1 17.2 1.0 C1C A:HEM501 3.1 17.8 1.0 CB A:CYS352 3.4 17.2 0.4 CB A:CYS352 3.4 17.2 0.6 CHD A:HEM501 3.4 16.9 1.0 CHA A:HEM501 3.4 19.8 1.0 CHB A:HEM501 3.5 15.7 1.0 CHC A:HEM501 3.5 15.6 1.0 C2D A:HEM501 4.2 16.9 1.0 O A:HOH647 4.2 16.5 0.1 C3D A:HEM501 4.2 19.7 1.0 CA A:CYS352 4.2 17.9 0.6 CA A:CYS352 4.2 17.9 0.4 C2A A:HEM501 4.2 16.5 1.0 C3A A:HEM501 4.3 16.5 1.0 C3C A:HEM501 4.3 20.6 1.0 C3B A:HEM501 4.3 18.2 1.0 C2C A:HEM501 4.3 18.9 1.0 C2B A:HEM501 4.3 16.1 1.0 O3 A:GOL503 4.6 22.2 0.5 O A:HOH727 4.6 22.1 0.1 CA A:GLY240 4.7 16.7 1.0 O A:ALA239 4.8 19.6 1.0 C A:CYS352 5.0 17.4 1.0

Iron binding site 2 out of 4 in the Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:18.4 occ:0.60 FE A:HEM501 0.0 18.4 0.6 FE A:HEM501 0.0 18.5 0.4 N A:NO502 1.9 16.3 0.4 ND A:HEM501 2.0 19.3 0.6 ND A:HEM501 2.0 19.3 0.4 NA A:HEM501 2.0 17.9 0.6 NA A:HEM501 2.0 17.9 0.4 NB A:HEM501 2.0 17.6 0.6 NB A:HEM501 2.0 17.6 0.4 NC A:HEM501 2.1 20.0 0.4 NC A:HEM501 2.1 20.1 0.6 O A:HOH712 2.1 14.9 0.5 SG A:CYS352 2.2 18.6 0.4 SG A:CYS352 2.2 18.6 0.6 C1D A:HEM501 3.0 15.6 1.0 O A:NO502 3.0 20.4 0.4 C4D A:HEM501 3.0 19.2 1.0 C1A A:HEM501 3.0 18.4 1.0 C4A A:HEM501 3.0 16.4 1.0 C4C A:HEM501 3.1 19.8 1.0 C4B A:HEM501 3.1 16.4 1.0 C1B A:HEM501 3.1 17.2 1.0 C1C A:HEM501 3.1 17.8 1.0 CB A:CYS352 3.3 17.2 0.4 CB A:CYS352 3.3 17.2 0.6 CHD A:HEM501 3.4 16.9 1.0 CHA A:HEM501 3.4 19.8 1.0 CHB A:HEM501 3.4 15.7 1.0 CHC A:HEM501 3.5 15.6 1.0 C2D A:HEM501 4.2 16.9 1.0 CA A:CYS352 4.2 17.9 0.6 CA A:CYS352 4.2 17.9 0.4 O A:HOH647 4.2 16.5 0.1 C3D A:HEM501 4.2 19.7 1.0 C2A A:HEM501 4.2 16.5 1.0 C3A A:HEM501 4.3 16.5 1.0 C3B A:HEM501 4.3 18.2 1.0 C3C A:HEM501 4.3 20.6 1.0 C2C A:HEM501 4.3 18.9 1.0 C2B A:HEM501 4.3 16.1 1.0 O3 A:GOL503 4.6 22.2 0.5 O A:HOH727 4.6 22.1 0.1 CA A:GLY240 4.7 16.7 1.0 O A:ALA239 4.8 19.6 1.0 C A:CYS352 5.0 17.4 1.0

Iron binding site 3 out of 4 in the Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:20.6 occ:0.40 FE B:HEM501 0.0 20.6 0.4 FE B:HEM501 0.0 20.3 0.6 N B:NO502 1.9 20.4 0.4 ND B:HEM501 2.0 20.8 0.6 ND B:HEM501 2.0 20.8 0.4 NA B:HEM501 2.0 19.2 0.6 NA B:HEM501 2.0 19.2 0.4 NB B:HEM501 2.1 19.4 0.4 NB B:HEM501 2.1 19.4 0.6 NC B:HEM501 2.1 18.7 0.4 NC B:HEM501 2.1 18.7 0.6 O B:HOH693 2.2 19.5 0.5 SG B:CYS352 2.3 18.1 0.4 SG B:CYS352 2.3 18.0 0.6 O B:NO502 2.9 22.3 0.4 C1D B:HEM501 3.0 21.0 1.0 C4D B:HEM501 3.0 20.5 1.0 C4A B:HEM501 3.0 19.5 1.0 C1A B:HEM501 3.0 18.8 1.0 C4C B:HEM501 3.1 20.6 1.0 C1B B:HEM501 3.1 18.5 1.0 C4B B:HEM501 3.1 16.7 1.0 C1C B:HEM501 3.1 18.3 1.0 CB B:CYS352 3.4 19.0 0.4 CB B:CYS352 3.4 19.0 0.6 CHD B:HEM501 3.4 21.0 1.0 CHB B:HEM501 3.4 16.3 1.0 CHA B:HEM501 3.4 22.2 1.0 CHC B:HEM501 3.5 20.0 1.0 CA B:CYS352 4.2 18.2 0.4 CA B:CYS352 4.2 18.2 0.6 C2D B:HEM501 4.2 21.0 1.0 C3D B:HEM501 4.2 17.1 1.0 C3A B:HEM501 4.2 21.5 1.0 C2A B:HEM501 4.2 20.4 1.0 C3B B:HEM501 4.3 23.4 1.0 C3C B:HEM501 4.3 22.0 1.0 C2B B:HEM501 4.3 18.6 1.0 C2C B:HEM501 4.4 16.2 1.0 O B:HOH661 4.5 22.5 0.1 O3 B:GOL503 4.5 22.4 0.5 CA B:GLY240 4.7 24.4 1.0 O B:ALA239 4.8 29.5 1.0 C3 B:GOL503 4.9 22.1 0.5 C2 B:GOL503 4.9 18.6 0.5 C B:CYS352 5.0 19.6 1.0

Iron binding site 4 out of 4 in the Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Reaction Intermediate of Cytochrome P450 No Reductase (P450NOR) Determined By Xfel within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:20.3 occ:0.60 FE B:HEM501 0.0 20.3 0.6 FE B:HEM501 0.0 20.6 0.4 N B:NO502 1.9 20.4 0.4 ND B:HEM501 2.0 20.8 0.6 ND B:HEM501 2.0 20.8 0.4 NA B:HEM501 2.0 19.2 0.6 NA B:HEM501 2.0 19.2 0.4 NB B:HEM501 2.1 19.4 0.4 NB B:HEM501 2.1 19.4 0.6 NC B:HEM501 2.1 18.7 0.4 NC B:HEM501 2.1 18.7 0.6 O B:HOH693 2.2 19.5 0.5 SG B:CYS352 2.2 18.1 0.4 SG B:CYS352 2.2 18.0 0.6 O B:NO502 3.0 22.3 0.4 C4A B:HEM501 3.0 19.5 1.0 C1D B:HEM501 3.0 21.0 1.0 C4D B:HEM501 3.0 20.5 1.0 C1A B:HEM501 3.0 18.8 1.0 C1B B:HEM501 3.1 18.5 1.0 C4C B:HEM501 3.1 20.6 1.0 C4B B:HEM501 3.1 16.7 1.0 C1C B:HEM501 3.1 18.3 1.0 CB B:CYS352 3.3 19.0 0.4 CB B:CYS352 3.3 19.0 0.6 CHB B:HEM501 3.4 16.3 1.0 CHD B:HEM501 3.4 21.0 1.0 CHA B:HEM501 3.4 22.2 1.0 CHC B:HEM501 3.5 20.0 1.0 CA B:CYS352 4.2 18.2 0.4 CA B:CYS352 4.2 18.2 0.6 C3D B:HEM501 4.2 17.1 1.0 C2D B:HEM501 4.2 21.0 1.0 C3A B:HEM501 4.2 21.5 1.0 C2A B:HEM501 4.2 20.4 1.0 C3B B:HEM501 4.3 23.4 1.0 C2B B:HEM501 4.3 18.6 1.0 C3C B:HEM501 4.3 22.0 1.0 C2C B:HEM501 4.4 16.2 1.0 O B:HOH661 4.5 22.5 0.1 O3 B:GOL503 4.6 22.4 0.5 CA B:GLY240 4.7 24.4 1.0 O B:ALA239 4.9 29.5 1.0 C3 B:GOL503 4.9 22.1 0.5 C B:CYS352 4.9 19.6 1.0 C2 B:GOL503 5.0 18.6 0.5

T.Nomura, H.Sugimoto, T.Tosha, M.Kubo, Y.Shiro. Coordination and Electronic Structures of Short-Lived Intermediate in No Reduction By Cytochrome P450 No Reductase As Characterized By Time-Resolved Ir Spectroscopy and Xfel Crystallography Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2101481118