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Iron in PDB 7coh: Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

All present enzymatic activity of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State:
7.1.1.9;

Protein crystallography data

The structure of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 7coh was solved by K.Shinzawa-Itoh, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.998, 204.193, 177.759, 90, 90, 90
R / Rfree (%) 14.9 / 17

Other elements in 7coh:

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

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

Iron Binding Sites:

The binding sites of Iron atom in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 7coh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 7coh:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7coh

Go back to Iron Binding Sites List in 7coh
Iron binding site 1 out of 4 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:18.2
occ:1.00
 FE A:HEA515 0.0 18.2 1.0
NE2 A:HIS378 1.9 19.1 1.0
NC A:HEA515 2.0 17.6 1.0
NE2 A:HIS61 2.0 19.4 1.0
NA A:HEA515 2.0 18.6 1.0
NB A:HEA515 2.0 17.1 1.0
ND A:HEA515 2.0 17.6 1.0
CE1 A:HIS378 3.0 20.7 1.0
CE1 A:HIS61 3.0 18.6 1.0
CD2 A:HIS378 3.0 17.6 1.0
CD2 A:HIS61 3.0 17.9 1.0
C4A A:HEA515 3.0 18.0 1.0
C4C A:HEA515 3.0 16.6 1.0
C1B A:HEA515 3.0 18.1 1.0
C1C A:HEA515 3.0 17.2 1.0
C1D A:HEA515 3.0 16.6 1.0
C1A A:HEA515 3.1 18.2 1.0
C4B A:HEA515 3.1 18.0 1.0
C4D A:HEA515 3.1 16.4 1.0
CHC A:HEA515 3.4 17.7 1.0
CHB A:HEA515 3.4 18.4 1.0
CHD A:HEA515 3.4 16.9 1.0
CHA A:HEA515 3.4 18.0 1.0
ND1 A:HIS378 4.1 18.2 1.0
ND1 A:HIS61 4.1 18.0 1.0
CG A:HIS61 4.1 17.6 1.0
CG A:HIS378 4.2 16.0 1.0
C3A A:HEA515 4.2 18.2 1.0
C2C A:HEA515 4.3 17.5 1.0
C3B A:HEA515 4.3 17.6 1.0
C2A A:HEA515 4.3 18.2 1.0
C3C A:HEA515 4.3 16.9 1.0
C2B A:HEA515 4.3 18.6 1.0
C3D A:HEA515 4.3 16.4 1.0
C2D A:HEA515 4.3 16.6 1.0
CE1 A:PHE377 4.8 17.8 1.0

Iron binding site 2 out of 4 in 7coh

Go back to Iron Binding Sites List in 7coh
Iron binding site 2 out of 4 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:17.4
occ:1.00
 FE A:HEA516 0.0 17.4 1.0
NC A:HEA516 2.0 17.1 1.0
NA A:HEA516 2.0 16.9 1.0
ND A:HEA516 2.0 17.3 1.0
NB A:HEA516 2.0 17.0 1.0
NE2 A:HIS376 2.1 17.2 1.0
O1 A:PER520 2.3 20.9 1.0
C4C A:HEA516 3.0 15.4 1.0
C4A A:HEA516 3.0 17.0 1.0
C1C A:HEA516 3.0 23.8 1.0
C1D A:HEA516 3.0 16.0 1.0
C1A A:HEA516 3.0 16.5 1.0
C1B A:HEA516 3.0 16.7 1.0
C4D A:HEA516 3.1 16.6 1.0
C4B A:HEA516 3.1 17.5 1.0
CE1 A:HIS376 3.1 18.2 1.0
CD2 A:HIS376 3.2 16.9 1.0
CHA A:HEA516 3.4 16.9 1.0
CHD A:HEA516 3.4 16.3 1.0
CHB A:HEA516 3.5 17.5 1.0
CHC A:HEA516 3.5 23.8 1.0
O2 A:PER520 3.9 26.7 1.0
C2A A:HEA516 4.2 17.1 1.0
C2C A:HEA516 4.2 18.4 1.0
ND1 A:HIS376 4.3 17.8 1.0
C3C A:HEA516 4.3 17.4 1.0
C3A A:HEA516 4.3 16.8 1.0
C3B A:HEA516 4.3 17.1 1.0
CG A:HIS376 4.3 17.2 1.0
C2D A:HEA516 4.3 16.1 1.0
C3D A:HEA516 4.3 16.4 1.0
C2B A:HEA516 4.4 17.5 1.0
CU A:CU517 4.8 17.9 1.0
CG2 A:VAL243 5.0 19.0 1.0

Iron binding site 3 out of 4 in 7coh

Go back to Iron Binding Sites List in 7coh
Iron binding site 3 out of 4 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:21.6
occ:1.00
 FE N:HEA515 0.0 21.6 1.0
NE2 N:HIS61 1.9 21.1 1.0
NA N:HEA515 2.0 21.7 1.0
NE2 N:HIS378 2.0 22.0 1.0
NB N:HEA515 2.0 20.8 1.0
NC N:HEA515 2.0 20.8 1.0
ND N:HEA515 2.0 20.3 1.0
CE1 N:HIS61 2.9 22.9 1.0
CD2 N:HIS61 2.9 21.2 1.0
CE1 N:HIS378 2.9 21.2 1.0
C1C N:HEA515 3.0 21.3 1.0
CD2 N:HIS378 3.0 20.2 1.0
C4A N:HEA515 3.0 21.9 1.0
C1B N:HEA515 3.1 22.2 1.0
C4C N:HEA515 3.1 19.7 1.0
C1A N:HEA515 3.1 21.1 1.0
C4B N:HEA515 3.1 21.7 1.0
C1D N:HEA515 3.1 21.8 1.0
C4D N:HEA515 3.1 20.8 1.0
CHC N:HEA515 3.4 21.3 1.0
CHB N:HEA515 3.4 21.9 1.0
CHD N:HEA515 3.4 20.9 1.0
CHA N:HEA515 3.5 22.3 1.0
ND1 N:HIS61 4.1 21.8 1.0
ND1 N:HIS378 4.1 21.7 1.0
CG N:HIS61 4.1 20.9 1.0
CG N:HIS378 4.2 19.4 1.0
C2A N:HEA515 4.3 22.2 1.0
C3A N:HEA515 4.3 21.6 1.0
C2C N:HEA515 4.3 20.9 1.0
C3B N:HEA515 4.3 21.9 1.0
C2B N:HEA515 4.3 22.8 1.0
C3C N:HEA515 4.3 21.1 1.0
C3D N:HEA515 4.3 21.2 1.0
C2D N:HEA515 4.3 20.6 1.0
CE1 N:PHE377 4.8 20.8 1.0

Iron binding site 4 out of 4 in 7coh

Go back to Iron Binding Sites List in 7coh
Iron binding site 4 out of 4 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:19.7
occ:1.00
 FE N:HEA516 0.0 19.7 1.0
ND N:HEA516 2.0 19.9 1.0
NB N:HEA516 2.0 19.3 1.0
NA N:HEA516 2.0 18.8 1.0
NC N:HEA516 2.0 19.0 1.0
NE2 N:HIS376 2.1 20.7 1.0
O1 N:PER520 2.3 19.9 1.0
C1D N:HEA516 3.0 18.8 1.0
C1B N:HEA516 3.0 19.7 1.0
C4C N:HEA516 3.0 20.0 1.0
C4A N:HEA516 3.0 19.4 1.0
C1C N:HEA516 3.0 18.5 1.0
C4D N:HEA516 3.1 20.1 1.0
C1A N:HEA516 3.1 18.7 1.0
C4B N:HEA516 3.1 18.6 1.0
CE1 N:HIS376 3.1 21.8 1.0
CD2 N:HIS376 3.2 20.6 1.0
CHD N:HEA516 3.4 20.2 1.0
CHA N:HEA516 3.4 19.5 1.0
CHC N:HEA516 3.4 19.2 1.0
CHB N:HEA516 3.5 19.1 1.0
O2 N:PER520 3.8 26.4 1.0
ND1 N:HIS376 4.3 20.2 1.0
C2A N:HEA516 4.3 19.3 1.0
C3D N:HEA516 4.3 19.9 1.0
C2C N:HEA516 4.3 18.5 1.0
CG N:HIS376 4.3 20.2 1.0
C3A N:HEA516 4.3 19.1 1.0
C2D N:HEA516 4.3 19.6 1.0
C3B N:HEA516 4.3 20.4 1.0
C2B N:HEA516 4.3 20.0 1.0
C3C N:HEA516 4.4 19.4 1.0
CU N:CU517 4.8 20.0 1.0
CG2 N:VAL243 4.9 19.6 1.0

Reference:

K.Shinzawa-Itoh, M.Hatanaka, K.Fujita, N.Yano, Y.Ogasawara, J.Iwata, E.Yamashita, T.Tsukihara, S.Yoshikawa, K.Muramoto. The 1.3-A Resolution Structure of Bovine Cytochrome C Oxidase Suggests A Dimerization Mechanism Biochim.Biophys.Acta 2021.
ISSN: ISSN 0006-3002
DOI: 10.1016/J.BBADVA.2021.100009
Page generated: Thu Aug 8 03:11:53 2024

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