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Iron in PDB 5y5i: Time-Resolved Sfx Structure of Cytochrome P450NOR: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data

Enzymatic activity of Time-Resolved Sfx Structure of Cytochrome P450NOR: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data

All present enzymatic activity of Time-Resolved Sfx Structure of Cytochrome P450NOR: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data:
1.7.1.14;

Protein crystallography data

The structure of Time-Resolved Sfx Structure of Cytochrome P450NOR: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data, PDB code: 5y5i 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) 41.05 / 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 (%) 14.8 / 19.6

Iron Binding Sites:

The binding sites of Iron atom in the Time-Resolved Sfx Structure of Cytochrome P450NOR: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data (pdb code 5y5i). 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: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data, PDB code: 5y5i:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5y5i

Go back to Iron Binding Sites List in 5y5i
Iron binding site 1 out of 2 in the Time-Resolved Sfx Structure of Cytochrome P450NOR: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data


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: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:29.0
occ:1.00
 FE A:HEM501 0.0 29.0 1.0
N A:NO502 1.7 31.5 0.4
NA A:HEM501 2.0 25.2 1.0
ND A:HEM501 2.0 26.6 1.0
NC A:HEM501 2.1 28.8 1.0
NB A:HEM501 2.1 26.1 1.0
SG A:CYS352 2.3 28.2 1.0
O A:HOH710 2.4 34.1 0.6
O A:NO502 2.8 36.2 0.4
C1A A:HEM501 3.0 29.1 1.0
C4A A:HEM501 3.0 30.2 1.0
C1D A:HEM501 3.0 29.0 1.0
C4D A:HEM501 3.0 27.6 1.0
C4C A:HEM501 3.0 28.6 1.0
C1B A:HEM501 3.1 28.2 1.0
C4B A:HEM501 3.1 25.6 1.0
C1C A:HEM501 3.1 30.3 1.0
CB A:CYS352 3.3 27.9 1.0
CHD A:HEM501 3.4 26.9 1.0
CHB A:HEM501 3.4 24.5 1.0
CHA A:HEM501 3.4 30.1 1.0
CHC A:HEM501 3.5 26.8 1.0
CA A:CYS352 4.2 28.8 1.0
C2A A:HEM501 4.2 26.2 1.0
C3A A:HEM501 4.2 28.4 1.0
C2D A:HEM501 4.2 33.1 1.0
C3D A:HEM501 4.3 29.9 1.0
C3C A:HEM501 4.3 27.0 1.0
C2B A:HEM501 4.3 30.3 1.0
C3B A:HEM501 4.3 28.2 1.0
C2C A:HEM501 4.3 30.0 1.0
CA A:GLY240 4.8 30.8 1.0
C A:CYS352 4.9 29.3 1.0

Iron binding site 2 out of 2 in 5y5i

Go back to Iron Binding Sites List in 5y5i
Iron binding site 2 out of 2 in the Time-Resolved Sfx Structure of Cytochrome P450NOR: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data


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: 20 Ms After Photo- Irradiation of Caged No in the Presence of Nadh (No-Bound State), Light Data within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.5
occ:1.00
 FE B:HEM501 0.0 30.5 1.0
N B:NO502 1.7 31.9 0.5
NA B:HEM501 2.0 28.7 1.0
ND B:HEM501 2.0 30.3 1.0
NB B:HEM501 2.1 25.4 1.0
NC B:HEM501 2.1 28.0 1.0
SG B:CYS352 2.3 25.3 1.0
O B:HOH677 2.4 33.0 0.5
O B:NO502 2.8 34.9 0.5
C4A B:HEM501 3.0 28.0 1.0
C1A B:HEM501 3.0 31.1 1.0
C4D B:HEM501 3.0 29.6 1.0
C1D B:HEM501 3.0 27.2 1.0
C1B B:HEM501 3.1 28.6 1.0
C4C B:HEM501 3.1 26.2 1.0
C4B B:HEM501 3.1 27.0 1.0
C1C B:HEM501 3.1 26.2 1.0
CB B:CYS352 3.2 27.5 1.0
CHA B:HEM501 3.4 27.6 1.0
CHB B:HEM501 3.4 25.0 1.0
CHD B:HEM501 3.4 25.9 1.0
CHC B:HEM501 3.5 26.6 1.0
CA B:CYS352 4.1 29.3 1.0
C3A B:HEM501 4.2 29.0 1.0
C2A B:HEM501 4.2 29.1 1.0
C2D B:HEM501 4.2 29.2 1.0
C3D B:HEM501 4.2 28.4 1.0
C3C B:HEM501 4.3 28.1 1.0
C3B B:HEM501 4.3 24.6 1.0
C2B B:HEM501 4.3 28.6 1.0
C2C B:HEM501 4.3 27.5 1.0
C B:CYS352 4.9 27.2 1.0
CA B:GLY240 4.9 32.0 1.0
O2 B:GOL503 5.0 43.5 0.8
N B:ILE353 5.0 28.8 1.0

Reference:

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
Page generated: Tue Aug 6 12:39:02 2024

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