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Iron in PDB 7ypy: Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy was solved by A.Shimada, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.96 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.938, 204.4, 177.896, 90, 90, 90
R / Rfree (%) 15.9 / 17.7

Other elements in 7ypy:

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution (pdb code 7ypy). 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 Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7ypy

Go back to Iron Binding Sites List in 7ypy
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:19.0
occ:1.00
 FE A:HEA601 0.0 19.0 1.0
NC A:HEA601 2.0 17.8 1.0
NE2 A:HIS61 2.0 18.5 1.0
NA A:HEA601 2.0 17.7 1.0
NB A:HEA601 2.0 20.3 1.0
NE2 A:HIS378 2.0 18.2 1.0
ND A:HEA601 2.0 18.8 1.0
C4A A:HEA601 2.9 17.5 1.0
CE1 A:HIS61 2.9 19.6 1.0
C4C A:HEA601 3.0 17.4 1.0
CE1 A:HIS378 3.0 19.5 1.0
C4D A:HEA601 3.0 17.2 1.0
CD2 A:HIS378 3.0 20.2 1.0
CD2 A:HIS61 3.0 20.0 1.0
C1B A:HEA601 3.0 18.0 1.0
C4B A:HEA601 3.0 18.5 1.0
C1D A:HEA601 3.1 17.5 1.0
C1C A:HEA601 3.1 17.9 1.0
C1A A:HEA601 3.1 17.9 1.0
CHC A:HEA601 3.4 18.3 1.0
CHD A:HEA601 3.4 18.5 1.0
CHA A:HEA601 3.4 18.1 1.0
CHB A:HEA601 3.4 20.9 1.0
ND1 A:HIS61 4.1 19.3 1.0
ND1 A:HIS378 4.1 17.1 1.0
CG A:HIS61 4.2 20.3 1.0
CG A:HIS378 4.2 16.5 1.0
C3A A:HEA601 4.2 18.6 1.0
C2C A:HEA601 4.2 18.1 1.0
C2A A:HEA601 4.2 19.5 1.0
C2B A:HEA601 4.3 18.0 1.0
C3C A:HEA601 4.3 17.1 1.0
C2D A:HEA601 4.3 18.6 1.0
C3D A:HEA601 4.3 18.1 1.0
C3B A:HEA601 4.3 16.7 1.0
CE2 A:PHE377 4.8 18.4 1.0

Iron binding site 2 out of 4 in 7ypy

Go back to Iron Binding Sites List in 7ypy
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:18.7
occ:1.00
 FE A:HEA602 0.0 18.7 1.0
NC A:HEA602 2.0 17.5 1.0
NA A:HEA602 2.0 17.7 1.0
ND A:HEA602 2.0 17.9 1.0
NB A:HEA602 2.0 18.9 1.0
NE2 A:HIS376 2.1 18.4 1.0
O1 A:PER606 2.2 16.4 1.0
C4A A:HEA602 3.0 17.4 1.0
C4C A:HEA602 3.0 16.3 1.0
C1D A:HEA602 3.1 19.0 1.0
C1B A:HEA602 3.1 18.4 1.0
C4B A:HEA602 3.1 18.8 1.0
CE1 A:HIS376 3.1 19.1 1.0
C4D A:HEA602 3.1 17.3 1.0
C1A A:HEA602 3.1 17.2 1.0
C1C A:HEA602 3.1 17.3 1.0
CD2 A:HIS376 3.1 18.1 1.0
CHB A:HEA602 3.4 19.7 1.0
CHA A:HEA602 3.4 19.2 1.0
CHC A:HEA602 3.4 17.7 1.0
CHD A:HEA602 3.4 18.9 1.0
O2 A:PER606 3.6 23.6 1.0
ND1 A:HIS376 4.2 18.4 1.0
C2A A:HEA602 4.3 18.7 1.0
C3A A:HEA602 4.3 18.0 1.0
C2D A:HEA602 4.3 18.1 1.0
CG A:HIS376 4.3 18.1 1.0
C3C A:HEA602 4.3 17.2 1.0
C3B A:HEA602 4.3 17.5 1.0
C2C A:HEA602 4.3 17.2 1.0
C3D A:HEA602 4.3 16.8 1.0
C2B A:HEA602 4.3 18.1 1.0
CU A:CU603 4.8 19.1 1.0

Iron binding site 3 out of 4 in 7ypy

Go back to Iron Binding Sites List in 7ypy
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:22.8
occ:1.00
 FE N:HEA601 0.0 22.8 1.0
NC N:HEA601 1.9 22.2 1.0
NA N:HEA601 2.0 23.3 1.0
NE2 N:HIS61 2.0 23.2 1.0
ND N:HEA601 2.0 21.6 1.0
NE2 N:HIS378 2.0 22.9 1.0
NB N:HEA601 2.0 22.4 1.0
CE1 N:HIS378 3.0 25.4 1.0
C4B N:HEA601 3.0 22.6 1.0
CE1 N:HIS61 3.0 24.2 1.0
C4D N:HEA601 3.0 22.4 1.0
C4A N:HEA601 3.0 23.8 1.0
CD2 N:HIS61 3.0 23.8 1.0
C4C N:HEA601 3.0 21.6 1.0
CD2 N:HIS378 3.0 22.2 1.0
C1D N:HEA601 3.0 22.9 1.0
C1C N:HEA601 3.1 22.4 1.0
C1A N:HEA601 3.1 20.7 1.0
C1B N:HEA601 3.1 23.1 1.0
CHD N:HEA601 3.4 22.3 1.0
CHC N:HEA601 3.4 22.1 1.0
CHB N:HEA601 3.5 24.3 1.0
CHA N:HEA601 3.5 24.3 1.0
ND1 N:HIS378 4.1 23.1 1.0
ND1 N:HIS61 4.1 23.8 1.0
CG N:HIS61 4.1 23.9 1.0
CG N:HIS378 4.2 22.2 1.0
C2D N:HEA601 4.2 21.4 1.0
C3A N:HEA601 4.2 22.3 1.0
C2B N:HEA601 4.2 23.1 1.0
C3B N:HEA601 4.2 22.0 1.0
C3D N:HEA601 4.2 21.2 1.0
C3C N:HEA601 4.3 21.8 1.0
C2C N:HEA601 4.3 22.0 1.0
C2A N:HEA601 4.3 22.9 1.0
CE2 N:PHE377 4.8 21.8 1.0

Iron binding site 4 out of 4 in 7ypy

Go back to Iron Binding Sites List in 7ypy
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:21.4
occ:1.00
 FE N:HEA602 0.0 21.4 1.0
NA N:HEA602 2.0 19.8 1.0
NC N:HEA602 2.0 20.5 1.0
ND N:HEA602 2.0 20.6 1.0
NE2 N:HIS376 2.1 21.2 1.0
NB N:HEA602 2.1 19.9 1.0
O2 N:PER606 2.2 19.8 1.0
C4A N:HEA602 3.0 19.2 1.0
C1D N:HEA602 3.1 21.2 1.0
C4C N:HEA602 3.1 20.2 1.0
CE1 N:HIS376 3.1 22.7 1.0
C1B N:HEA602 3.1 23.2 1.0
C1C N:HEA602 3.1 19.4 1.0
CD2 N:HIS376 3.1 21.0 1.0
C4D N:HEA602 3.1 21.4 1.0
C1A N:HEA602 3.1 21.1 1.0
C4B N:HEA602 3.1 18.8 1.0
CHA N:HEA602 3.4 21.2 1.0
CHD N:HEA602 3.5 21.9 1.0
CHC N:HEA602 3.5 20.2 1.0
CHB N:HEA602 3.5 20.9 1.0
O1 N:PER606 3.6 26.8 1.0
ND1 N:HIS376 4.2 22.3 1.0
C2D N:HEA602 4.2 20.6 1.0
CG N:HIS376 4.2 20.0 1.0
C3A N:HEA602 4.3 20.3 1.0
C2C N:HEA602 4.3 20.4 1.0
C3B N:HEA602 4.3 20.0 1.0
C2A N:HEA602 4.3 21.0 1.0
C3D N:HEA602 4.3 20.1 1.0
C2B N:HEA602 4.3 21.8 1.0
C3C N:HEA602 4.3 19.9 1.0
CU N:CU603 4.8 21.6 1.0
CG2 N:VAL243 5.0 20.5 1.0

Reference:

N.Yano, K.Muramoto, A.Shimada, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J. Biol. Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770
Page generated: Fri Aug 9 12:27:20 2024

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