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Iron in PDB 1occ: Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

Enzymatic activity of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

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

Protein crystallography data

The structure of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1occ was solved by T.Tsukihara, H.Aoyama, E.Yamashita, T.Tomizaki, H.Yamaguchi, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25.2

Other elements in 1occ:

The structure of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State also contains other interesting chemical elements:

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

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 1occ

Go back to Iron Binding Sites List in 1occ
Iron binding site 1 out of 4 in the Structure of 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 Structure 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:9.8
occ:1.00
FE A:HEA515 0.0 9.8 1.0
NE2 A:HIS61 1.8 7.0 1.0
NE2 A:HIS378 1.9 7.0 1.0
NB A:HEA515 1.9 13.1 1.0
NA A:HEA515 1.9 20.1 1.0
ND A:HEA515 2.0 9.7 1.0
NC A:HEA515 2.0 22.6 1.0
CE1 A:HIS378 2.6 7.0 1.0
CE1 A:HIS61 2.7 13.2 1.0
C1B A:HEA515 2.9 12.2 1.0
CD2 A:HIS61 2.9 9.3 1.0
C4A A:HEA515 3.0 15.2 1.0
C1D A:HEA515 3.0 14.3 1.0
C4B A:HEA515 3.0 19.0 1.0
C4C A:HEA515 3.0 17.6 1.0
C1A A:HEA515 3.1 10.3 1.0
C4D A:HEA515 3.1 15.1 1.0
C1C A:HEA515 3.1 17.1 1.0
CD2 A:HIS378 3.1 8.6 1.0
CHB A:HEA515 3.3 11.5 1.0
CHD A:HEA515 3.4 16.3 1.0
CHA A:HEA515 3.5 9.4 1.0
CHC A:HEA515 3.5 13.9 1.0
ND1 A:HIS378 3.9 11.0 1.0
ND1 A:HIS61 4.0 13.6 1.0
CG A:HIS61 4.1 8.7 1.0
C2B A:HEA515 4.2 16.0 1.0
C3A A:HEA515 4.2 13.5 1.0
CG A:HIS378 4.2 7.0 1.0
C2A A:HEA515 4.2 9.1 1.0
C2D A:HEA515 4.3 18.3 1.0
C3B A:HEA515 4.3 17.7 1.0
C3C A:HEA515 4.3 18.0 1.0
C3D A:HEA515 4.3 18.0 1.0
C2C A:HEA515 4.3 18.8 1.0

Iron binding site 2 out of 4 in 1occ

Go back to Iron Binding Sites List in 1occ
Iron binding site 2 out of 4 in the Structure of 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 Structure 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:8.0
occ:1.00
FE A:HEA516 0.0 8.0 1.0
ND A:HEA516 1.9 7.6 1.0
NB A:HEA516 2.0 10.9 1.0
NC A:HEA516 2.0 16.3 1.0
NA A:HEA516 2.0 14.8 1.0
NE2 A:HIS376 2.1 7.0 1.0
C1D A:HEA516 3.0 11.3 1.0
C4D A:HEA516 3.0 14.8 1.0
CE1 A:HIS376 3.0 10.5 1.0
C1B A:HEA516 3.0 14.2 1.0
C4B A:HEA516 3.0 14.2 1.0
C4C A:HEA516 3.1 13.7 1.0
C4A A:HEA516 3.1 14.3 1.0
C1C A:HEA516 3.1 13.1 1.0
C1A A:HEA516 3.1 7.0 1.0
CD2 A:HIS376 3.2 9.2 1.0
CHD A:HEA516 3.4 12.9 1.0
CHB A:HEA516 3.4 17.8 1.0
CHA A:HEA516 3.4 8.6 1.0
CHC A:HEA516 3.4 10.2 1.0
C3D A:HEA516 4.2 13.9 1.0
C2D A:HEA516 4.2 12.4 1.0
C2B A:HEA516 4.3 11.5 1.0
ND1 A:HIS376 4.3 7.0 1.0
C3B A:HEA516 4.3 16.1 1.0
C3A A:HEA516 4.3 7.0 1.0
C3C A:HEA516 4.3 14.3 1.0
CG A:HIS376 4.3 7.0 1.0
C2C A:HEA516 4.3 15.4 1.0
C2A A:HEA516 4.4 7.0 1.0
CU A:CU517 4.7 15.3 1.0
CE1 A:HIS240 4.9 27.2 1.0

Iron binding site 3 out of 4 in 1occ

Go back to Iron Binding Sites List in 1occ
Iron binding site 3 out of 4 in the Structure of 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 Structure 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:9.8
occ:1.00
FE N:HEA515 0.0 9.8 1.0
NE2 N:HIS61 1.8 7.0 1.0
NE2 N:HIS378 1.9 7.0 1.0
NB N:HEA515 1.9 13.1 1.0
NA N:HEA515 1.9 20.1 1.0
ND N:HEA515 2.0 9.7 1.0
NC N:HEA515 2.0 22.6 1.0
CE1 N:HIS378 2.6 7.0 1.0
CE1 N:HIS61 2.7 13.2 1.0
C1B N:HEA515 2.9 12.2 1.0
CD2 N:HIS61 2.9 9.3 1.0
C4A N:HEA515 3.0 15.2 1.0
C1D N:HEA515 3.0 14.3 1.0
C4C N:HEA515 3.0 17.6 1.0
C4B N:HEA515 3.0 19.0 1.0
C1A N:HEA515 3.1 10.3 1.0
C4D N:HEA515 3.1 15.1 1.0
C1C N:HEA515 3.1 17.1 1.0
CD2 N:HIS378 3.1 8.6 1.0
CHB N:HEA515 3.3 11.5 1.0
CHD N:HEA515 3.4 16.3 1.0
CHA N:HEA515 3.5 9.4 1.0
CHC N:HEA515 3.5 13.9 1.0
ND1 N:HIS378 3.9 11.0 1.0
ND1 N:HIS61 4.0 13.6 1.0
CG N:HIS61 4.1 8.7 1.0
C2B N:HEA515 4.2 16.0 1.0
C3A N:HEA515 4.2 13.5 1.0
CG N:HIS378 4.2 7.0 1.0
C2A N:HEA515 4.2 9.1 1.0
C2D N:HEA515 4.3 18.3 1.0
C3B N:HEA515 4.3 17.7 1.0
C3C N:HEA515 4.3 18.0 1.0
C3D N:HEA515 4.3 18.0 1.0
C2C N:HEA515 4.3 18.8 1.0

Iron binding site 4 out of 4 in 1occ

Go back to Iron Binding Sites List in 1occ
Iron binding site 4 out of 4 in the Structure of 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 Structure 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:8.0
occ:1.00
FE N:HEA516 0.0 8.0 1.0
ND N:HEA516 1.9 7.6 1.0
NB N:HEA516 2.0 10.9 1.0
NC N:HEA516 2.0 16.3 1.0
NA N:HEA516 2.0 14.8 1.0
NE2 N:HIS376 2.1 7.0 1.0
C1D N:HEA516 3.0 11.3 1.0
C4D N:HEA516 3.0 14.8 1.0
CE1 N:HIS376 3.0 10.5 1.0
C1B N:HEA516 3.0 14.2 1.0
C4B N:HEA516 3.0 14.2 1.0
C4C N:HEA516 3.1 13.7 1.0
C4A N:HEA516 3.1 14.3 1.0
C1C N:HEA516 3.1 13.1 1.0
C1A N:HEA516 3.1 7.0 1.0
CD2 N:HIS376 3.2 9.2 1.0
CHD N:HEA516 3.4 12.9 1.0
CHB N:HEA516 3.4 17.8 1.0
CHA N:HEA516 3.4 8.6 1.0
CHC N:HEA516 3.4 10.2 1.0
C3D N:HEA516 4.2 13.9 1.0
C2D N:HEA516 4.2 12.4 1.0
C2B N:HEA516 4.3 11.5 1.0
ND1 N:HIS376 4.3 7.0 1.0
C3B N:HEA516 4.3 16.1 1.0
C3A N:HEA516 4.3 7.0 1.0
C3C N:HEA516 4.3 14.3 1.0
CG N:HIS376 4.3 7.0 1.0
C2C N:HEA516 4.3 15.4 1.0
C2A N:HEA516 4.4 7.0 1.0
CU N:CU517 4.7 15.3 1.0
CE1 N:HIS240 4.9 27.2 1.0

Reference:

T.Tsukihara, H.Aoyama, E.Yamashita, T.Tomizaki, H.Yamaguchi, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, S.Yoshikawa. The Whole Structure of the 13-Subunit Oxidized Cytochrome C Oxidase at 2.8 A. Science V. 272 1136 1996.
ISSN: ISSN 0036-8075
PubMed: 8638158
Page generated: Sat Aug 3 12:16:11 2024

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