Iron in PDB 5y5l: Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State)

All present enzymatic activity of Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State):
1.7.1.14;

The structure of Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State), PDB code: 5y5l 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 (%)	14.6 / 19.3

The binding sites of Iron atom in the Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State) (pdb code 5y5l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State), PDB code: 5y5l:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:37.6 occ:1.00 FE A:HEM501 0.0 37.6 1.0 NA A:HEM501 1.9 34.3 1.0 ND A:HEM501 1.9 34.8 1.0 NB A:HEM501 2.1 32.4 1.0 NC A:HEM501 2.1 36.2 1.0 SG A:CYS352 2.2 35.5 1.0 O A:HOH683 2.4 36.9 0.7 C1D A:HEM501 2.9 35.4 1.0 C4D A:HEM501 2.9 35.0 1.0 C1A A:HEM501 2.9 34.4 1.0 C4A A:HEM501 3.0 35.0 1.0 C4B A:HEM501 3.1 32.8 1.0 C4C A:HEM501 3.1 35.8 1.0 C1B A:HEM501 3.1 33.5 1.0 C1C A:HEM501 3.2 37.7 1.0 CB A:CYS352 3.4 32.2 1.0 CHA A:HEM501 3.4 35.1 1.0 CHD A:HEM501 3.4 34.2 1.0 CHB A:HEM501 3.4 32.1 1.0 CHC A:HEM501 3.5 34.6 1.0 C2A A:HEM501 4.2 34.1 1.0 CA A:CYS352 4.2 35.1 1.0 C3A A:HEM501 4.2 37.8 1.0 C2D A:HEM501 4.2 40.7 1.0 C3D A:HEM501 4.2 37.2 1.0 C3C A:HEM501 4.3 35.9 1.0 C3B A:HEM501 4.3 35.6 1.0 C2B A:HEM501 4.4 36.6 1.0 C2C A:HEM501 4.4 35.6 1.0 CA A:GLY240 4.9 37.3 1.0 O A:ALA239 4.9 46.0 1.0 C A:CYS352 5.0 37.9 1.0

Iron binding site 2 out of 2 in the Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Time-Resolved Sfx Structure of Cytochrome P450NOR: Dark-2 Data in the Absence of Nadh (Resting State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:38.6 occ:1.00 FE B:HEM501 0.0 38.6 1.0 NA B:HEM501 1.9 36.9 1.0 ND B:HEM501 1.9 39.0 1.0 NC B:HEM501 2.1 36.3 1.0 NB B:HEM501 2.1 34.9 1.0 SG B:CYS352 2.3 33.9 1.0 O B:HOH693 2.4 39.6 0.9 C1A B:HEM501 2.9 37.4 1.0 C4D B:HEM501 2.9 37.9 1.0 C1D B:HEM501 2.9 34.8 1.0 C4A B:HEM501 2.9 34.6 1.0 C1B B:HEM501 3.1 35.7 1.0 C4C B:HEM501 3.1 36.0 1.0 C4B B:HEM501 3.1 37.1 1.0 C1C B:HEM501 3.2 35.8 1.0 CB B:CYS352 3.3 35.0 1.0 CHA B:HEM501 3.3 37.0 1.0 CHB B:HEM501 3.3 34.9 1.0 CHD B:HEM501 3.4 33.7 1.0 CHC B:HEM501 3.5 35.2 1.0 CA B:CYS352 4.1 36.2 1.0 C2D B:HEM501 4.2 35.5 1.0 C2A B:HEM501 4.2 37.7 1.0 C3A B:HEM501 4.2 37.3 1.0 C3D B:HEM501 4.2 35.6 1.0 C3C B:HEM501 4.3 36.9 1.0 C2C B:HEM501 4.4 35.3 1.0 C3B B:HEM501 4.4 35.3 1.0 C2B B:HEM501 4.4 36.8 1.0 O B:HOH763 4.7 57.0 1.0 C B:CYS352 4.9 34.1 1.0 CA B:GLY240 4.9 40.4 1.0 N B:ILE353 5.0 37.3 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