Iron in PDB 2y69: Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen, PDB code: 2y69 was solved by V.R.I.Kaila, E.Oksanen, A.Goldman, M.I.Verkhovsky, D.Sundholm, M.Wikstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.15 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.5

The structure of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen also contains other interesting chemical elements:

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

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen (pdb code 2y69). 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 Re-Refined with Molecular Oxygen, PDB code: 2y69:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe515 b:26.2 occ:1.00 FE A:HEA515 0.0 26.2 1.0 NE2 A:HIS378 1.9 24.5 1.0 NE2 A:HIS61 1.9 22.7 1.0 ND A:HEA515 2.0 25.4 1.0 NB A:HEA515 2.0 26.3 1.0 NA A:HEA515 2.0 28.7 1.0 NC A:HEA515 2.0 24.8 1.0 CE1 A:HIS61 2.9 26.0 1.0 CE1 A:HIS378 2.9 28.1 1.0 CD2 A:HIS378 3.0 26.9 1.0 C4A A:HEA515 3.0 30.2 1.0 C4C A:HEA515 3.0 25.1 1.0 C1D A:HEA515 3.0 25.1 1.0 C4D A:HEA515 3.0 23.6 1.0 C1B A:HEA515 3.0 29.3 1.0 CD2 A:HIS61 3.0 27.6 1.0 C1C A:HEA515 3.0 25.5 1.0 C4B A:HEA515 3.1 26.9 1.0 C1A A:HEA515 3.1 27.7 1.0 CHB A:HEA515 3.4 28.8 1.0 CHD A:HEA515 3.4 24.0 1.0 CHC A:HEA515 3.4 22.0 1.0 CHA A:HEA515 3.5 24.4 1.0 ND1 A:HIS378 4.0 24.2 1.0 ND1 A:HIS61 4.0 24.9 1.0 CG A:HIS378 4.1 25.2 1.0 CG A:HIS61 4.1 25.7 1.0 C3A A:HEA515 4.3 29.4 1.0 C2D A:HEA515 4.3 24.3 1.0 C3C A:HEA515 4.3 24.9 1.0 C3D A:HEA515 4.3 26.2 1.0 C2B A:HEA515 4.3 26.0 1.0 C2C A:HEA515 4.3 26.0 1.0 C3B A:HEA515 4.4 25.7 1.0 C2A A:HEA515 4.4 30.3 1.0 CE1 A:PHE377 5.0 29.2 1.0

Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe516 b:26.4 occ:1.00 FE A:HEA516 0.0 26.4 1.0 ND A:HEA516 2.0 24.0 1.0 NA A:HEA516 2.0 24.9 1.0 NB A:HEA516 2.0 26.0 1.0 NE2 A:HIS376 2.0 25.8 1.0 NC A:HEA516 2.0 27.4 1.0 O2 A:OXY1515 2.2 32.3 1.0 CE1 A:HIS376 2.9 31.2 1.0 C4D A:HEA516 3.0 26.4 1.0 C1A A:HEA516 3.0 24.1 1.0 C4A A:HEA516 3.0 22.2 1.0 C4B A:HEA516 3.0 26.3 1.0 C1C A:HEA516 3.0 25.1 1.0 C1D A:HEA516 3.0 26.8 1.0 C4C A:HEA516 3.0 22.7 1.0 CD2 A:HIS376 3.0 29.2 1.0 C1B A:HEA516 3.1 26.1 1.0 O1 A:OXY1515 3.1 41.0 1.0 CHA A:HEA516 3.4 23.9 1.0 CHC A:HEA516 3.4 25.2 1.0 CHB A:HEA516 3.4 23.2 1.0 CHD A:HEA516 3.5 21.1 1.0 ND1 A:HIS376 4.1 29.8 1.0 CG A:HIS376 4.2 28.1 1.0 C3A A:HEA516 4.2 23.4 1.0 C2D A:HEA516 4.3 23.6 1.0 C2A A:HEA516 4.3 26.3 1.0 C3D A:HEA516 4.3 24.6 1.0 C3B A:HEA516 4.3 27.0 1.0 C2B A:HEA516 4.3 25.6 1.0 C2C A:HEA516 4.3 29.0 1.0 C3C A:HEA516 4.3 25.5 1.0 CU A:CU517 4.9 28.5 1.0

Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe515 b:31.4 occ:1.00 FE N:HEA515 0.0 31.4 1.0 NE2 N:HIS378 1.9 22.4 1.0 NE2 N:HIS61 2.0 23.8 1.0 NC N:HEA515 2.0 30.6 1.0 NA N:HEA515 2.0 34.4 1.0 NB N:HEA515 2.0 35.6 1.0 ND N:HEA515 2.0 32.2 1.0 CD2 N:HIS378 2.9 31.2 1.0 CD2 N:HIS61 2.9 33.3 1.0 CE1 N:HIS378 2.9 29.2 1.0 C4C N:HEA515 3.0 45.9 1.0 C4A N:HEA515 3.0 36.2 1.0 CE1 N:HIS61 3.0 38.4 1.0 C1B N:HEA515 3.0 32.6 1.0 C1A N:HEA515 3.0 39.8 1.0 C1C N:HEA515 3.0 40.5 1.0 C1D N:HEA515 3.0 54.2 1.0 C4B N:HEA515 3.1 35.9 1.0 C4D N:HEA515 3.1 29.3 1.0 CHB N:HEA515 3.4 40.0 1.0 CHD N:HEA515 3.4 36.0 1.0 CHC N:HEA515 3.5 32.0 1.0 CHA N:HEA515 3.5 34.7 1.0 ND1 N:HIS378 4.0 27.0 1.0 CG N:HIS378 4.0 22.1 1.0 ND1 N:HIS61 4.1 28.3 1.0 CG N:HIS61 4.1 29.0 1.0 C3A N:HEA515 4.2 44.0 1.0 C3C N:HEA515 4.2 35.7 1.0 C2B N:HEA515 4.3 53.7 1.0 C2C N:HEA515 4.3 38.6 1.0 C2A N:HEA515 4.3 45.6 1.0 C3B N:HEA515 4.4 34.4 1.0 C2D N:HEA515 4.4 26.6 1.0 C3D N:HEA515 4.4 25.6 1.0 CE1 N:PHE377 5.0 33.8 1.0

Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe516 b:34.7 occ:1.00 FE N:HEA516 0.0 34.7 1.0 NC N:HEA516 2.0 37.5 1.0 ND N:HEA516 2.0 33.3 1.0 NB N:HEA516 2.0 35.8 1.0 NA N:HEA516 2.0 39.4 1.0 NE2 N:HIS376 2.0 44.4 1.0 O1 N:OXY1515 2.4 31.2 1.0 CE1 N:HIS376 2.9 44.7 1.0 C4D N:HEA516 3.0 32.2 1.0 C1C N:HEA516 3.0 27.9 1.0 C1A N:HEA516 3.0 29.0 1.0 C4A N:HEA516 3.0 26.3 1.0 O2 N:OXY1515 3.0 33.9 1.0 C1B N:HEA516 3.0 29.6 1.0 C4C N:HEA516 3.0 30.8 1.0 C4B N:HEA516 3.0 32.8 1.0 C1D N:HEA516 3.0 36.3 1.0 CD2 N:HIS376 3.1 34.6 1.0 CHA N:HEA516 3.4 26.9 1.0 CHC N:HEA516 3.4 31.1 1.0 CHB N:HEA516 3.4 21.4 1.0 CHD N:HEA516 3.5 30.0 1.0 ND1 N:HIS376 4.1 34.6 1.0 CG N:HIS376 4.2 35.8 1.0 C3A N:HEA516 4.3 27.1 1.0 C3C N:HEA516 4.3 34.5 1.0 C2C N:HEA516 4.3 40.6 1.0 C2D N:HEA516 4.3 26.5 1.0 C2B N:HEA516 4.3 31.7 1.0 C3D N:HEA516 4.3 29.2 1.0 C3B N:HEA516 4.3 29.2 1.0 C2A N:HEA516 4.3 31.1 1.0 CU N:CU517 4.9 32.4 1.0 CG2 N:VAL243 4.9 34.6 1.0

V.R.I.Kaila, E.Oksanen, A.Goldman, D.A.Bloch, M.I.Verkhovsky, D.Sundholm, M.Wikstrom. A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome C Oxidase. Biochim.Biophys.Acta V.1807 769 2011.
ISSN: ISSN 0006-3002
PubMed: 21211513
DOI: 10.1016/J.BBABIO.2010.12.016