Iron in PDB 5x1f: Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K

All present enzymatic activity of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K:
1.9.3.1;

The structure of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K, PDB code: 5x1f was solved by A.Shimada, M.Kubo, S.Baba, K.Yamashita, K.Hirata, G.Ueno, T.Nomura, T.Kimura, K.Shinzawa-Itoh, J.Baba, K.Hatano, Y.Eto, A.Miyamoto, H.Murakami, T.Kumasaka, S.Owada, K.Tono, M.Yabashi, Y.Yamaguchi, S.Yanagisawa, M.Sakaguchi, T.Ogura, R.Komiya, J.Yan, E.Yamashita, M.Yamamoto, H.Ago, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	184.806, 208.488, 177.885, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.9

The structure of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms
Copper	(Cu)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Iron atom in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K (pdb code 5x1f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K, PDB code: 5x1f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:40.4 occ:1.00 FE A:HEA601 0.0 40.4 1.0 NE2 A:HIS378 2.0 36.1 1.0 NC A:HEA601 2.0 42.1 1.0 NE2 A:HIS61 2.0 44.8 1.0 NB A:HEA601 2.0 43.5 1.0 ND A:HEA601 2.1 43.4 1.0 NA A:HEA601 2.1 41.0 1.0 CE1 A:HIS378 2.9 39.7 1.0 CD2 A:HIS61 2.9 37.6 1.0 CD2 A:HIS378 3.0 34.9 1.0 C4C A:HEA601 3.0 41.2 1.0 C4B A:HEA601 3.0 41.1 1.0 C1C A:HEA601 3.1 38.8 1.0 C1B A:HEA601 3.1 40.3 1.0 C1D A:HEA601 3.1 41.4 1.0 C4D A:HEA601 3.1 41.1 1.0 C4A A:HEA601 3.1 43.3 1.0 C1A A:HEA601 3.1 40.2 1.0 CE1 A:HIS61 3.1 44.8 1.0 CHD A:HEA601 3.4 41.5 1.0 CHA A:HEA601 3.4 39.6 1.0 CHC A:HEA601 3.5 35.1 1.0 CHB A:HEA601 3.5 36.8 1.0 ND1 A:HIS378 4.1 36.6 1.0 O A:HOH779 4.1 96.1 1.0 CG A:HIS378 4.1 37.4 1.0 CG A:HIS61 4.2 37.5 1.0 ND1 A:HIS61 4.2 39.1 1.0 C3C A:HEA601 4.2 40.6 1.0 C3B A:HEA601 4.2 41.3 1.0 C2C A:HEA601 4.3 42.5 1.0 C2B A:HEA601 4.3 42.2 1.0 C3A A:HEA601 4.3 39.1 1.0 C3D A:HEA601 4.3 39.0 1.0 C2D A:HEA601 4.3 39.0 1.0 C2A A:HEA601 4.3 37.2 1.0 CE1 A:PHE377 4.8 35.6 1.0

Iron binding site 2 out of 4 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:38.9 occ:1.00 FE A:HEA602 0.0 38.9 1.0 NC A:HEA602 2.0 38.7 1.0 NB A:HEA602 2.1 35.9 1.0 NA A:HEA602 2.1 40.4 1.0 C A:CMO606 2.1 34.1 1.0 ND A:HEA602 2.1 37.9 1.0 NE2 A:HIS376 2.2 38.9 1.0 C1C A:HEA602 3.0 41.5 1.0 C4C A:HEA602 3.0 41.6 1.0 C1B A:HEA602 3.0 37.8 1.0 C4B A:HEA602 3.1 37.4 1.0 C1A A:HEA602 3.1 38.9 1.0 C4D A:HEA602 3.1 34.9 1.0 C4A A:HEA602 3.1 38.9 1.0 O A:CMO606 3.1 48.4 1.0 CD2 A:HIS376 3.1 37.2 1.0 C1D A:HEA602 3.1 39.5 1.0 CE1 A:HIS376 3.3 38.3 1.0 CHB A:HEA602 3.4 37.9 1.0 CHC A:HEA602 3.4 39.2 1.0 CHA A:HEA602 3.4 36.7 1.0 CHD A:HEA602 3.5 37.6 1.0 C3C A:HEA602 4.2 42.2 1.0 C2C A:HEA602 4.2 40.3 1.0 C3B A:HEA602 4.3 37.8 1.0 C2B A:HEA602 4.3 37.8 1.0 C3A A:HEA602 4.3 37.0 1.0 C2A A:HEA602 4.3 38.7 1.0 C3D A:HEA602 4.3 39.7 1.0 CG A:HIS376 4.3 34.6 1.0 ND1 A:HIS376 4.4 36.0 1.0 C2D A:HEA602 4.4 39.3 1.0 CG2 A:VAL243 5.0 43.1 1.0

Iron binding site 3 out of 4 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe601 b:47.0 occ:1.00 FE N:HEA601 0.0 47.0 1.0 NE2 N:HIS378 2.0 42.3 1.0 NA N:HEA601 2.1 52.1 1.0 ND N:HEA601 2.1 41.9 1.0 NC N:HEA601 2.1 45.4 1.0 NB N:HEA601 2.1 52.6 1.0 NE2 N:HIS61 2.1 49.2 1.0 CD2 N:HIS378 2.9 39.0 1.0 CD2 N:HIS61 2.9 39.7 1.0 C1D N:HEA601 3.0 42.5 1.0 C4A N:HEA601 3.1 50.4 1.0 CE1 N:HIS378 3.1 41.4 1.0 C4B N:HEA601 3.1 47.1 1.0 C1C N:HEA601 3.1 44.0 1.0 C4C N:HEA601 3.1 43.8 1.0 C1A N:HEA601 3.1 53.7 1.0 C4D N:HEA601 3.1 43.7 1.0 C1B N:HEA601 3.1 51.6 1.0 CE1 N:HIS61 3.2 47.8 1.0 CHB N:HEA601 3.4 48.8 1.0 CHD N:HEA601 3.4 43.3 1.0 CHA N:HEA601 3.4 47.7 1.0 CHC N:HEA601 3.5 42.0 1.0 CG N:HIS378 4.2 41.8 1.0 CG N:HIS61 4.2 44.8 1.0 ND1 N:HIS378 4.2 43.8 1.0 ND1 N:HIS61 4.3 47.0 1.0 C3B N:HEA601 4.3 52.2 1.0 C2D N:HEA601 4.3 43.4 1.0 C2A N:HEA601 4.3 44.4 1.0 C3A N:HEA601 4.3 45.9 1.0 C3C N:HEA601 4.3 41.8 1.0 C2C N:HEA601 4.3 44.9 1.0 C3D N:HEA601 4.3 42.6 1.0 C2B N:HEA601 4.3 50.2 1.0 O N:HOH791 4.5 0.8 1.0 CE1 N:PHE377 4.8 47.5 1.0

Iron binding site 4 out of 4 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe602 b:45.0 occ:1.00 FE N:HEA602 0.0 45.0 1.0 NC N:HEA602 2.0 43.5 1.0 NA N:HEA602 2.0 44.7 1.0 NB N:HEA602 2.1 43.2 1.0 ND N:HEA602 2.1 41.4 1.0 NE2 N:HIS376 2.2 45.9 1.0 C N:CMO606 2.4 43.8 1.0 O N:CMO606 2.6 49.3 1.0 C1C N:HEA602 3.0 46.0 1.0 C4C N:HEA602 3.0 45.5 1.0 C1A N:HEA602 3.0 47.9 1.0 C4A N:HEA602 3.0 44.1 1.0 C4B N:HEA602 3.0 38.4 1.0 C1B N:HEA602 3.1 41.2 1.0 C4D N:HEA602 3.1 42.1 1.0 C1D N:HEA602 3.1 44.2 1.0 CD2 N:HIS376 3.1 47.7 1.0 CE1 N:HIS376 3.2 42.1 1.0 CHC N:HEA602 3.4 41.1 1.0 CHA N:HEA602 3.4 39.8 1.0 CHD N:HEA602 3.4 40.2 1.0 CHB N:HEA602 3.5 41.2 1.0 C3A N:HEA602 4.2 46.7 1.0 C3C N:HEA602 4.2 44.5 1.0 C2C N:HEA602 4.2 41.2 1.0 C3B N:HEA602 4.2 44.8 1.0 C2A N:HEA602 4.2 47.1 1.0 C2B N:HEA602 4.2 45.9 1.0 ND1 N:HIS376 4.3 43.8 1.0 CG N:HIS376 4.3 45.8 1.0 C3D N:HEA602 4.3 40.8 1.0 C2D N:HEA602 4.4 41.4 1.0 CG2 N:VAL243 4.9 53.8 1.0

A.Shimada, M.Kubo, S.Baba, K.Yamashita, K.Hirata, G.Ueno, T.Nomura, T.Kimura, K.Shinzawa-Itoh, J.Baba, K.Hatano, Y.Eto, A.Miyamoto, H.Murakami, T.Kumasaka, S.Owada, K.Tono, M.Yabashi, Y.Yamaguchi, S.Yanagisawa, M.Sakaguchi, T.Ogura, R.Komiya, J.Yan, E.Yamashita, M.Yamamoto, H.Ago, S.Yoshikawa, T.Tsukihara. A Nanosecond Time-Resolved Xfel Analysis of Structural Changes Associated with Co Release From Cytochrome C Oxidase. Sci Adv V. 3 03042 2017.
ISSN: ESSN 2375-2548
PubMed: 28740863
DOI: 10.1126/SCIADV.1603042