Iron in PDB 5y5m: Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State)

All present enzymatic activity of Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State):
1.7.1.14;

The structure of Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State), PDB code: 5y5m was solved by T.Tosha, T.Nomura, T.Nishida, N.Saeki, K.Okubayashi, R.Yamagiwa, M.Sugahara, T.Nakane, K.Yamashita, K.Hirata, G.Ueno, T.Kimura, T.Hisano, K.Muramoto, H.Sawai, H.Takeda, E.Mizohata, A.Yamashita, Y.Kanematsu, Y.Takano, E.Nango, R.Tanaka, O.Nureki, Y.Ikemoto, H.Murakami, S.Owada, K.Tono, M.Yabashi, M.Yamamoto, H.Ago, S.Iwata, H.Sugimoto, Y.Shiro, M.Kubo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.600, 102.300, 73.700, 90.00, 92.60, 90.00
R / Rfree (%)	16.8 / 21.8

The binding sites of Iron atom in the Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State) (pdb code 5y5m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State), PDB code: 5y5m:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:36.6 occ:1.00 FE A:HEM501 0.0 36.6 1.0 NA A:HEM501 2.0 33.5 1.0 ND A:HEM501 2.0 34.6 1.0 NB A:HEM501 2.1 32.0 1.0 NC A:HEM501 2.1 35.0 1.0 SG A:CYS352 2.2 36.8 1.0 O A:HOH673 2.4 34.5 0.6 C1A A:HEM501 3.0 38.1 1.0 C4A A:HEM501 3.0 38.2 1.0 C1D A:HEM501 3.0 36.3 1.0 C4D A:HEM501 3.0 37.0 1.0 C4C A:HEM501 3.1 36.3 1.0 C1B A:HEM501 3.1 34.5 1.0 C4B A:HEM501 3.1 32.8 1.0 C1C A:HEM501 3.1 37.1 1.0 CB A:CYS352 3.3 34.1 1.0 CHA A:HEM501 3.4 36.3 1.0 CHB A:HEM501 3.4 30.6 1.0 CHD A:HEM501 3.4 32.8 1.0 CHC A:HEM501 3.5 33.7 1.0 CA A:CYS352 4.2 38.5 1.0 C2A A:HEM501 4.2 34.1 1.0 C3A A:HEM501 4.2 36.8 1.0 C2D A:HEM501 4.2 40.6 1.0 C3D A:HEM501 4.3 38.5 1.0 C3C A:HEM501 4.3 36.5 1.0 C2B A:HEM501 4.3 36.8 1.0 C2C A:HEM501 4.3 37.2 1.0 C3B A:HEM501 4.3 34.0 1.0 O A:ALA239 4.9 44.0 1.0 CA A:GLY240 4.9 37.9 1.0 C A:CYS352 4.9 36.8 1.0

Iron binding site 2 out of 2 in the Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sfx Structure of Cytochrome P450NOR: A Complete Dark Data Without Pump Laser (Resting State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:39.4 occ:1.00 FE B:HEM501 0.0 39.4 1.0 NA B:HEM501 2.0 38.9 1.0 ND B:HEM501 2.0 39.0 1.0 NC B:HEM501 2.1 36.8 1.0 NB B:HEM501 2.1 32.6 1.0 SG B:CYS352 2.3 35.2 1.0 O B:HOH729 2.4 36.6 0.7 C1A B:HEM501 3.0 38.4 1.0 C4A B:HEM501 3.0 37.8 1.0 C4D B:HEM501 3.0 39.5 1.0 C1D B:HEM501 3.0 39.4 1.0 C4C B:HEM501 3.1 39.8 1.0 C1B B:HEM501 3.1 32.6 1.0 C4B B:HEM501 3.1 38.3 1.0 C1C B:HEM501 3.1 35.4 1.0 CB B:CYS352 3.3 34.6 1.0 CHA B:HEM501 3.3 37.6 1.0 CHB B:HEM501 3.4 33.8 1.0 CHD B:HEM501 3.4 34.6 1.0 CHC B:HEM501 3.5 35.6 1.0 CA B:CYS352 4.2 38.3 1.0 C2A B:HEM501 4.2 39.0 1.0 C3A B:HEM501 4.2 37.2 1.0 C3D B:HEM501 4.2 36.7 1.0 C2D B:HEM501 4.2 40.9 1.0 C3C B:HEM501 4.3 35.6 1.0 C2C B:HEM501 4.3 34.6 1.0 C2B B:HEM501 4.3 36.1 1.0 C3B B:HEM501 4.3 36.9 1.0 O B:HOH744 4.8 54.5 1.0 CA B:GLY240 4.8 38.5 1.0 C B:CYS352 5.0 36.2 1.0

T.Tosha, T.Nomura, T.Nishida, N.Saeki, K.Okubayashi, R.Yamagiwa, M.Sugahara, T.Nakane, K.Yamashita, K.Hirata, G.Ueno, T.Kimura, T.Hisano, K.Muramoto, H.Sawai, H.Takeda, E.Mizohata, A.Yamashita, Y.Kanematsu, Y.Takano, E.Nango, R.Tanaka, O.Nureki, O.Shoji, Y.Ikemoto, H.Murakami, S.Owada, K.Tono, M.Yabashi, M.Yamamoto, H.Ago, S.Iwata, H.Sugimoto, Y.Shiro, M.Kubo. Capturing An Initial Intermediate During the P450NOR Enzymatic Reaction Using Time-Resolved Xfel Crystallography and Caged-Substrate. Nat Commun V. 8 1585 2017.
ISSN: ESSN 2041-1723
PubMed: 29147002
DOI: 10.1038/S41467-017-01702-1