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Iron in PDB 8h8r: Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State, PDB code: 8h8r was solved by K.Muramoto, K.Shinzawa-Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.8, 205.7, 177.9, 90, 90, 90
R / Rfree (%) 12.2 / 15.3

Other elements in 8h8r:

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State (pdb code 8h8r). 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 the Calcium-Bound Fully Oxidized State, PDB code: 8h8r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8h8r

Go back to Iron Binding Sites List in 8h8r
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound 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 in the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:27.8
occ:1.00
 FE A:HEA601 0.0 27.8 1.0
ND A:HEA601 2.0 27.3 1.0
NB A:HEA601 2.0 26.7 1.0
NC A:HEA601 2.0 26.5 1.0
NA A:HEA601 2.0 26.6 1.0
NE2 A:HIS378 2.0 27.0 1.0
NE2 A:HIS61 2.0 27.2 1.0
C1C A:HEA601 3.0 28.7 1.0
CE1 A:HIS378 3.0 29.3 1.0
C1D A:HEA601 3.0 25.4 1.0
C1B A:HEA601 3.0 26.7 1.0
C4D A:HEA601 3.0 28.0 1.0
CE1 A:HIS61 3.0 28.5 1.0
C1A A:HEA601 3.0 29.7 1.0
CD2 A:HIS61 3.1 29.2 1.0
C4C A:HEA601 3.1 26.1 1.0
C4A A:HEA601 3.1 27.3 1.0
C4B A:HEA601 3.1 28.7 1.0
CD2 A:HIS378 3.1 28.6 1.0
CHC A:HEA601 3.4 25.9 1.0
CHA A:HEA601 3.4 25.2 1.0
CHD A:HEA601 3.5 26.3 1.0
CHB A:HEA601 3.5 29.6 1.0
ND1 A:HIS378 4.1 28.1 1.0
ND1 A:HIS61 4.1 27.5 1.0
CG A:HIS61 4.2 26.5 1.0
CG A:HIS378 4.2 27.6 1.0
C3A A:HEA601 4.3 27.3 1.0
C2D A:HEA601 4.3 25.1 1.0
C2C A:HEA601 4.3 26.8 1.0
C2A A:HEA601 4.3 27.8 1.0
C3D A:HEA601 4.3 27.1 1.0
C2B A:HEA601 4.3 28.3 1.0
C3C A:HEA601 4.3 26.6 1.0
C3B A:HEA601 4.3 28.0 1.0
CE1 A:PHE377 4.9 29.6 1.0

Iron binding site 2 out of 4 in 8h8r

Go back to Iron Binding Sites List in 8h8r
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound 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 in the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:27.9
occ:1.00
 FE A:HEA602 0.0 27.9 1.0
ND A:HEA602 2.0 27.4 1.0
NB A:HEA602 2.0 28.1 1.0
NA A:HEA602 2.0 26.2 1.0
NC A:HEA602 2.1 26.6 1.0
NE2 A:HIS376 2.2 28.0 1.0
O1 A:PER606 2.3 29.8 1.0
C4A A:HEA602 3.0 25.8 1.0
C4D A:HEA602 3.0 27.2 1.0
C1C A:HEA602 3.0 27.9 1.0
C1A A:HEA602 3.0 27.7 1.0
C4C A:HEA602 3.0 26.6 1.0
C4B A:HEA602 3.0 28.1 1.0
C1B A:HEA602 3.1 26.4 1.0
C1D A:HEA602 3.1 26.7 1.0
CD2 A:HIS376 3.1 29.3 1.0
CE1 A:HIS376 3.2 28.7 1.0
CHA A:HEA602 3.4 26.6 1.0
CHC A:HEA602 3.4 27.9 1.0
CHD A:HEA602 3.5 26.6 1.0
CHB A:HEA602 3.5 28.4 1.0
O2 A:PER606 3.8 35.0 1.0
ND1 A:HIS376 4.3 27.1 1.0
CG A:HIS376 4.3 29.5 1.0
C3A A:HEA602 4.3 26.4 1.0
C3D A:HEA602 4.3 26.1 1.0
C2D A:HEA602 4.3 27.8 1.0
C2A A:HEA602 4.3 24.9 1.0
C3C A:HEA602 4.3 27.4 1.0
C3B A:HEA602 4.3 27.2 1.0
C2C A:HEA602 4.3 26.8 1.0
C2B A:HEA602 4.4 27.3 1.0
CU A:CU603 4.9 28.6 1.0

Iron binding site 3 out of 4 in 8h8r

Go back to Iron Binding Sites List in 8h8r
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound 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 in the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:35.4
occ:1.00
 FE N:HEA603 0.0 35.4 1.0
NC N:HEA603 2.0 31.6 1.0
NB N:HEA603 2.0 35.6 1.0
ND N:HEA603 2.0 33.2 1.0
NA N:HEA603 2.0 34.0 1.0
NE2 N:HIS61 2.0 34.3 1.0
NE2 N:HIS378 2.1 36.6 1.0
C1B N:HEA603 3.0 34.0 1.0
C1A N:HEA603 3.0 34.9 1.0
CD2 N:HIS61 3.0 35.9 1.0
C1D N:HEA603 3.0 33.4 1.0
C4A N:HEA603 3.0 34.2 1.0
C4C N:HEA603 3.0 34.2 1.0
C1C N:HEA603 3.0 36.3 1.0
CD2 N:HIS378 3.0 35.6 1.0
C4D N:HEA603 3.1 34.3 1.0
C4B N:HEA603 3.1 36.6 1.0
CE1 N:HIS378 3.1 33.8 1.0
CE1 N:HIS61 3.1 38.9 1.0
CHB N:HEA603 3.4 36.9 1.0
CHA N:HEA603 3.4 35.4 1.0
CHD N:HEA603 3.4 33.3 1.0
CHC N:HEA603 3.4 33.6 1.0
CG N:HIS61 4.2 35.1 1.0
ND1 N:HIS378 4.2 36.2 1.0
ND1 N:HIS61 4.2 33.5 1.0
CG N:HIS378 4.2 33.2 1.0
C3A N:HEA603 4.3 34.5 1.0
C2A N:HEA603 4.3 34.8 1.0
C2B N:HEA603 4.3 35.3 1.0
C3C N:HEA603 4.3 34.1 1.0
C2C N:HEA603 4.3 35.4 1.0
C2D N:HEA603 4.3 32.9 1.0
C3B N:HEA603 4.3 35.1 1.0
C3D N:HEA603 4.4 33.0 1.0
CE1 N:PHE377 4.9 34.5 1.0

Iron binding site 4 out of 4 in 8h8r

Go back to Iron Binding Sites List in 8h8r
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound 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 in the Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe604

b:32.0
occ:1.00
 FE N:HEA604 0.0 32.0 1.0
NA N:HEA604 2.0 32.9 1.0
NB N:HEA604 2.0 31.6 1.0
NC N:HEA604 2.0 30.1 1.0
ND N:HEA604 2.0 31.5 1.0
NE2 N:HIS376 2.2 32.7 1.0
O1 N:PER608 2.3 33.9 1.0
C4C N:HEA604 3.0 31.9 1.0
C1A N:HEA604 3.0 32.3 1.0
C4D N:HEA604 3.0 32.2 1.0
C1C N:HEA604 3.0 31.8 1.0
C1B N:HEA604 3.1 30.8 1.0
C4B N:HEA604 3.1 32.8 1.0
C4A N:HEA604 3.1 28.4 1.0
C1D N:HEA604 3.1 33.1 1.0
CD2 N:HIS376 3.1 33.0 1.0
CE1 N:HIS376 3.2 33.7 1.0
CHA N:HEA604 3.4 31.8 1.0
CHC N:HEA604 3.4 29.8 1.0
CHD N:HEA604 3.4 31.7 1.0
CHB N:HEA604 3.5 33.3 1.0
O2 N:PER608 3.7 40.8 1.0
C3A N:HEA604 4.3 29.8 1.0
CG N:HIS376 4.3 33.7 1.0
ND1 N:HIS376 4.3 31.2 1.0
C2A N:HEA604 4.3 31.7 1.0
C3B N:HEA604 4.3 30.4 1.0
C2C N:HEA604 4.3 30.9 1.0
C3C N:HEA604 4.3 31.8 1.0
C3D N:HEA604 4.4 31.6 1.0
C2B N:HEA604 4.4 31.4 1.0
C2D N:HEA604 4.4 32.1 1.0
CU N:CU605 4.9 32.8 1.0

Reference:

K.Muramoto, K.Shinzawa-Itoh. Calcium-Bound Structure of Bovine Cytochrome C Oxidase. Biochim Biophys Acta 48956 2023BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 36708913
DOI: 10.1016/J.BBABIO.2023.148956
Page generated: Sat Aug 10 05:08:57 2024

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