Iron in PDB 2dyr: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 2dyr was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.7

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (pdb code 2dyr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 2dyr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe515 b:20.9 occ:1.00 FE A:HEA515 0.0 20.9 1.0 NE2 A:HIS378 1.9 13.4 1.0 NB A:HEA515 2.0 19.1 1.0 NE2 A:HIS61 2.0 13.4 1.0 NC A:HEA515 2.0 19.5 1.0 ND A:HEA515 2.0 20.4 1.0 NA A:HEA515 2.1 19.2 1.0 CE1 A:HIS378 2.8 17.9 1.0 CE1 A:HIS61 3.0 15.9 1.0 C1B A:HEA515 3.0 21.8 1.0 C4B A:HEA515 3.0 20.8 1.0 CD2 A:HIS61 3.0 19.1 1.0 C4C A:HEA515 3.0 20.4 1.0 C1C A:HEA515 3.1 20.7 1.0 CD2 A:HIS378 3.1 17.8 1.0 C4A A:HEA515 3.1 20.2 1.0 C1D A:HEA515 3.1 22.8 1.0 C4D A:HEA515 3.1 23.4 1.0 C1A A:HEA515 3.1 21.3 1.0 CHC A:HEA515 3.4 21.4 1.0 CHB A:HEA515 3.4 19.6 1.0 CHD A:HEA515 3.4 19.0 1.0 CHA A:HEA515 3.5 23.3 1.0 ND1 A:HIS378 4.0 17.6 1.0 ND1 A:HIS61 4.1 16.4 1.0 CG A:HIS378 4.1 16.2 1.0 CG A:HIS61 4.2 16.5 1.0 C2B A:HEA515 4.2 20.1 1.0 C3B A:HEA515 4.3 19.2 1.0 C3C A:HEA515 4.3 20.2 1.0 C2C A:HEA515 4.3 19.6 1.0 C3A A:HEA515 4.3 21.1 1.0 C2A A:HEA515 4.3 20.2 1.0 C3D A:HEA515 4.3 22.3 1.0 C2D A:HEA515 4.3 19.9 1.0 CE2 A:PHE377 5.0 19.9 1.0

Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe516 b:17.8 occ:1.00 FE A:HEA516 0.0 17.8 1.0 ND A:HEA516 1.9 19.2 1.0 NB A:HEA516 1.9 18.3 1.0 NA A:HEA516 2.0 19.0 1.0 NC A:HEA516 2.1 18.8 1.0 NE2 A:HIS376 2.1 17.8 1.0 CE1 A:HIS376 3.0 20.8 1.0 C4D A:HEA516 3.0 20.2 1.0 C1B A:HEA516 3.0 19.4 1.0 C4B A:HEA516 3.0 21.9 1.0 C1D A:HEA516 3.0 20.3 1.0 C4A A:HEA516 3.1 17.9 1.0 C1A A:HEA516 3.1 16.5 1.0 C1C A:HEA516 3.1 20.6 1.0 C4C A:HEA516 3.1 17.4 1.0 CD2 A:HIS376 3.2 18.5 1.0 CHB A:HEA516 3.4 21.3 1.0 CHA A:HEA516 3.4 17.2 1.0 CHC A:HEA516 3.4 21.6 1.0 CHD A:HEA516 3.5 17.2 1.0 ND1 A:HIS376 4.2 19.8 1.0 C2B A:HEA516 4.2 18.7 1.0 C3D A:HEA516 4.2 18.8 1.0 C3B A:HEA516 4.3 21.1 1.0 C2D A:HEA516 4.3 18.9 1.0 CG A:HIS376 4.3 19.4 1.0 C2A A:HEA516 4.3 17.6 1.0 C3A A:HEA516 4.3 17.8 1.0 C3C A:HEA516 4.4 17.8 1.0 C2C A:HEA516 4.4 21.3 1.0 CU A:CU517 5.0 20.0 1.0

Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe515 b:20.5 occ:1.00 FE N:HEA515 0.0 20.5 1.0 NE2 N:HIS61 1.9 16.2 1.0 NE2 N:HIS378 2.0 17.3 1.0 NB N:HEA515 2.0 23.3 1.0 NC N:HEA515 2.0 22.8 1.0 ND N:HEA515 2.0 22.8 1.0 NA N:HEA515 2.0 23.6 1.0 CE1 N:HIS378 2.9 18.3 1.0 CE1 N:HIS61 2.9 22.0 1.0 CD2 N:HIS61 2.9 21.8 1.0 C1B N:HEA515 3.0 23.6 1.0 C4C N:HEA515 3.0 25.2 1.0 C4D N:HEA515 3.0 24.7 1.0 C4B N:HEA515 3.1 24.1 1.0 C1A N:HEA515 3.1 25.1 1.0 C4A N:HEA515 3.1 24.9 1.0 C1D N:HEA515 3.1 24.7 1.0 C1C N:HEA515 3.1 24.1 1.0 CD2 N:HIS378 3.1 17.9 1.0 CHB N:HEA515 3.4 22.1 1.0 CHA N:HEA515 3.4 25.1 1.0 CHD N:HEA515 3.4 22.0 1.0 CHC N:HEA515 3.4 22.9 1.0 ND1 N:HIS61 4.1 17.7 1.0 ND1 N:HIS378 4.1 17.4 1.0 CG N:HIS61 4.1 21.6 1.0 CG N:HIS378 4.2 16.8 1.0 C2B N:HEA515 4.3 24.0 1.0 C2A N:HEA515 4.3 23.4 1.0 C3B N:HEA515 4.3 24.2 1.0 C3A N:HEA515 4.3 24.4 1.0 C3C N:HEA515 4.3 24.0 1.0 C3D N:HEA515 4.3 22.4 1.0 C2D N:HEA515 4.3 23.2 1.0 C2C N:HEA515 4.3 24.9 1.0 CE2 N:PHE377 4.8 21.8 1.0

Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe516 b:20.6 occ:1.00 FE N:HEA516 0.0 20.6 1.0 ND N:HEA516 1.9 18.9 1.0 NB N:HEA516 2.0 19.2 1.0 NC N:HEA516 2.0 22.2 1.0 NA N:HEA516 2.1 20.3 1.0 NE2 N:HIS376 2.2 22.2 1.0 C4D N:HEA516 3.0 19.4 1.0 C1D N:HEA516 3.0 22.6 1.0 C4B N:HEA516 3.0 21.7 1.0 C1B N:HEA516 3.1 21.0 1.0 C4C N:HEA516 3.1 22.8 1.0 C1C N:HEA516 3.1 20.8 1.0 C1A N:HEA516 3.1 19.1 1.0 CD2 N:HIS376 3.1 21.0 1.0 C4A N:HEA516 3.1 19.5 1.0 CE1 N:HIS376 3.2 24.0 1.0 CHD N:HEA516 3.4 23.6 1.0 CHA N:HEA516 3.4 17.8 1.0 CHC N:HEA516 3.4 21.9 1.0 CHB N:HEA516 3.5 19.8 1.0 C3D N:HEA516 4.2 18.4 1.0 C2D N:HEA516 4.2 19.7 1.0 C2B N:HEA516 4.3 17.6 1.0 C3B N:HEA516 4.3 19.2 1.0 CG N:HIS376 4.3 21.6 1.0 ND1 N:HIS376 4.3 21.2 1.0 C2C N:HEA516 4.3 22.6 1.0 C2A N:HEA516 4.4 18.8 1.0 C3C N:HEA516 4.4 22.7 1.0 C3A N:HEA516 4.4 18.8 1.0 CU N:CU517 5.0 21.4 1.0

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618