Iron in PDB 1ocz: Bovine Heart Cytochrome C Oxidase in Azide-Bound State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Azide-Bound State:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in Azide-Bound State, PDB code: 1ocz was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	189.200, 210.600, 178.500, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.5

The structure of Bovine Heart Cytochrome C Oxidase in Azide-Bound 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 in Azide-Bound State (pdb code 1ocz). 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 in Azide-Bound State, PDB code: 1ocz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound 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 in Azide-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe515 b:15.5 occ:1.00 FE A:HEA515 0.0 15.5 1.0 NE2 A:HIS378 1.9 7.0 1.0 CE1 A:HIS61 1.9 13.9 1.0 NB A:HEA515 1.9 26.3 1.0 NA A:HEA515 1.9 27.2 1.0 ND A:HEA515 1.9 23.2 1.0 NC A:HEA515 2.0 28.0 1.0 NE2 A:HIS61 2.5 19.4 1.0 CE1 A:HIS378 2.7 8.2 1.0 C1B A:HEA515 2.9 27.9 1.0 C4A A:HEA515 3.0 24.5 1.0 C1D A:HEA515 3.0 22.9 1.0 C1A A:HEA515 3.0 25.0 1.0 C4B A:HEA515 3.0 31.4 1.0 C4D A:HEA515 3.0 28.3 1.0 C1C A:HEA515 3.0 32.2 1.0 C4C A:HEA515 3.0 20.5 1.0 CD2 A:HIS378 3.1 7.0 1.0 ND1 A:HIS61 3.1 17.6 1.0 CHB A:HEA515 3.3 28.9 1.0 CHD A:HEA515 3.4 27.2 1.0 CHA A:HEA515 3.4 26.5 1.0 CHC A:HEA515 3.4 33.8 1.0 CD2 A:HIS61 3.9 7.0 1.0 ND1 A:HIS378 4.0 13.3 1.0 CG A:HIS61 4.1 11.1 1.0 C2B A:HEA515 4.1 34.6 1.0 CG A:HIS378 4.2 7.0 1.0 C2A A:HEA515 4.2 20.8 1.0 C3A A:HEA515 4.2 19.1 1.0 C2D A:HEA515 4.2 27.4 1.0 C3D A:HEA515 4.3 30.2 1.0 C3B A:HEA515 4.3 31.7 1.0 C3C A:HEA515 4.3 28.0 1.0 C2C A:HEA515 4.3 33.5 1.0

Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound 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 in Azide-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe516 b:9.6 occ:1.00 FE A:HEA516 0.0 9.6 1.0 NE2 A:HIS376 1.9 10.4 1.0 ND A:HEA516 1.9 7.0 1.0 NC A:HEA516 2.0 11.0 1.0 NB A:HEA516 2.0 7.0 1.0 N1 A:AZI520 2.0 21.1 1.0 NA A:HEA516 2.1 10.3 1.0 CE1 A:HIS376 2.7 7.3 1.0 C1D A:HEA516 2.9 10.8 1.0 C4D A:HEA516 3.0 18.0 1.0 C4C A:HEA516 3.0 10.7 1.0 C1B A:HEA516 3.0 7.0 1.0 C4A A:HEA516 3.0 12.8 1.0 C1C A:HEA516 3.0 9.4 1.0 C4B A:HEA516 3.1 12.8 1.0 C1A A:HEA516 3.1 7.0 1.0 N2 A:AZI520 3.1 33.2 1.0 CD2 A:HIS376 3.1 16.1 1.0 CHD A:HEA516 3.2 15.9 1.0 CHB A:HEA516 3.3 14.1 1.0 CHA A:HEA516 3.4 10.8 1.0 CHC A:HEA516 3.5 7.0 1.0 ND1 A:HIS376 4.0 11.5 1.0 CG A:HIS376 4.2 8.1 1.0 C2D A:HEA516 4.2 17.8 1.0 C3C A:HEA516 4.2 14.2 1.0 C3D A:HEA516 4.2 20.2 1.0 C2B A:HEA516 4.2 7.0 1.0 C2C A:HEA516 4.2 13.4 1.0 N3 A:AZI520 4.3 28.8 1.0 C3A A:HEA516 4.3 7.6 1.0 C3B A:HEA516 4.3 13.5 1.0 C2A A:HEA516 4.4 12.2 1.0

Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound 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 in Azide-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe515 b:24.9 occ:1.00 FE N:HEA515 0.0 24.9 1.0 CE1 N:HIS61 1.9 25.6 1.0 NA N:HEA515 1.9 31.9 1.0 ND N:HEA515 1.9 35.1 1.0 NE2 N:HIS378 2.0 27.0 1.0 NB N:HEA515 2.0 42.2 1.0 NC N:HEA515 2.0 33.7 1.0 NE2 N:HIS61 2.4 34.5 1.0 CE1 N:HIS378 2.8 20.8 1.0 C4D N:HEA515 3.0 40.8 1.0 C4A N:HEA515 3.0 35.3 1.0 C1A N:HEA515 3.0 35.9 1.0 C1D N:HEA515 3.0 33.1 1.0 C1B N:HEA515 3.0 41.9 1.0 C4C N:HEA515 3.0 34.3 1.0 C1C N:HEA515 3.1 37.1 1.0 ND1 N:HIS61 3.1 26.9 1.0 C4B N:HEA515 3.1 39.2 1.0 CD2 N:HIS378 3.2 24.6 1.0 CHD N:HEA515 3.3 36.3 1.0 CHA N:HEA515 3.4 37.4 1.0 CHB N:HEA515 3.4 33.4 1.0 CHC N:HEA515 3.5 35.8 1.0 CD2 N:HIS61 3.8 22.2 1.0 CG N:HIS61 4.0 21.4 1.0 ND1 N:HIS378 4.1 13.4 1.0 C2D N:HEA515 4.2 34.2 1.0 C2B N:HEA515 4.2 45.1 1.0 C2A N:HEA515 4.2 33.5 1.0 C3A N:HEA515 4.2 34.1 1.0 C3D N:HEA515 4.2 40.1 1.0 C3C N:HEA515 4.3 39.2 1.0 CG N:HIS378 4.3 19.9 1.0 C2C N:HEA515 4.3 41.0 1.0 C3B N:HEA515 4.3 38.3 1.0 CE1 N:PHE377 5.0 18.6 1.0

Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound 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 in Azide-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe516 b:17.9 occ:1.00 FE N:HEA516 0.0 17.9 1.0 NB N:HEA516 1.9 7.0 1.0 NC N:HEA516 2.0 10.5 1.0 NE2 N:HIS376 2.0 20.7 1.0 ND N:HEA516 2.0 16.0 1.0 NA N:HEA516 2.0 8.4 1.0 N1 N:AZI520 2.1 34.3 1.0 CE1 N:HIS376 2.7 25.6 1.0 C1B N:HEA516 2.9 15.2 1.0 C4A N:HEA516 3.0 16.6 1.0 C4B N:HEA516 3.0 14.4 1.0 C1C N:HEA516 3.0 16.0 1.0 C1D N:HEA516 3.0 21.6 1.0 C4C N:HEA516 3.0 16.6 1.0 C4D N:HEA516 3.1 11.0 1.0 C1A N:HEA516 3.1 10.7 1.0 CHB N:HEA516 3.2 15.0 1.0 CD2 N:HIS376 3.2 24.7 1.0 N2 N:AZI520 3.3 48.5 1.0 CHD N:HEA516 3.4 22.0 1.0 CHC N:HEA516 3.4 16.3 1.0 CHA N:HEA516 3.4 8.1 1.0 ND1 N:HIS376 4.0 25.3 1.0 C2B N:HEA516 4.2 17.1 1.0 C3A N:HEA516 4.2 19.1 1.0 C2C N:HEA516 4.2 19.0 1.0 C3C N:HEA516 4.2 20.3 1.0 C3B N:HEA516 4.3 16.2 1.0 C2D N:HEA516 4.3 18.8 1.0 CG N:HIS376 4.3 20.7 1.0 C3D N:HEA516 4.3 15.2 1.0 C2A N:HEA516 4.3 19.6 1.0 N3 N:AZI520 4.5 37.3 1.0

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723