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Iron in PDB 7cp5: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution, PDB code: 7cp5 was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.91 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.589, 203.218, 177.702, 90, 90, 90
R / Rfree (%) 16 / 18.9

Other elements in 7cp5:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution also contains other interesting chemical elements:

Copper (Cu) 6 atoms
Magnesium (Mg) 2 atoms
Sodium (Na) 4 atoms
Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution (pdb code 7cp5). 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution, PDB code: 7cp5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7cp5

Go back to Iron Binding Sites List in 7cp5
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:21.2
occ:1.00
 FE A:HEA601 0.0 21.2 1.0
NE2 A:HIS61 2.0 21.4 1.0
NE2 A:HIS378 2.0 20.7 1.0
ND A:HEA601 2.0 20.0 1.0
NC A:HEA601 2.0 20.1 1.0
NB A:HEA601 2.0 21.8 1.0
NA A:HEA601 2.0 22.0 1.0
CE1 A:HIS378 2.9 25.0 1.0
CE1 A:HIS61 3.0 25.4 1.0
CD2 A:HIS61 3.0 22.3 1.0
C4C A:HEA601 3.0 18.9 1.0
C4A A:HEA601 3.0 23.4 1.0
C4D A:HEA601 3.0 17.8 1.0
C1C A:HEA601 3.0 21.7 1.0
C1D A:HEA601 3.0 20.0 1.0
CD2 A:HIS378 3.0 22.7 1.0
C1A A:HEA601 3.1 22.2 1.0
C4B A:HEA601 3.1 20.9 1.0
C1B A:HEA601 3.1 19.7 1.0
CHB A:HEA601 3.4 22.7 1.0
CHC A:HEA601 3.4 17.8 1.0
CHD A:HEA601 3.5 18.7 1.0
CHA A:HEA601 3.5 21.5 1.0
ND1 A:HIS378 4.1 19.8 1.0
ND1 A:HIS61 4.1 23.7 1.0
CG A:HIS61 4.1 22.8 1.0
CG A:HIS378 4.2 21.4 1.0
C3A A:HEA601 4.2 24.2 1.0
C2C A:HEA601 4.2 22.9 1.0
C2A A:HEA601 4.2 19.1 1.0
C3C A:HEA601 4.2 17.4 1.0
C2D A:HEA601 4.3 19.3 1.0
C3D A:HEA601 4.3 19.3 1.0
C2B A:HEA601 4.3 23.0 1.0
C3B A:HEA601 4.3 19.1 1.0
OG A:SER382 4.8 68.8 0.2
CE1 A:PHE377 4.9 22.3 1.0

Iron binding site 2 out of 4 in 7cp5

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Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:21.6
occ:1.00
 FE A:HEA602 0.0 21.6 1.0
O A:HOH710 1.8 18.3 0.5
NB A:HEA602 2.0 21.7 1.0
NC A:HEA602 2.0 22.2 1.0
ND A:HEA602 2.0 22.6 1.0
NA A:HEA602 2.0 21.7 1.0
NE2 A:HIS376 2.1 21.1 1.0
O1 A:PER608 2.2 23.9 0.5
C4B A:HEA602 3.0 21.4 1.0
C4A A:HEA602 3.0 22.1 1.0
C1C A:HEA602 3.0 24.1 1.0
C4D A:HEA602 3.0 21.9 1.0
CE1 A:HIS376 3.0 22.2 1.0
C1A A:HEA602 3.0 21.2 1.0
C1B A:HEA602 3.1 20.8 1.0
C4C A:HEA602 3.1 18.7 1.0
C1D A:HEA602 3.1 19.9 1.0
CD2 A:HIS376 3.1 22.0 1.0
CHC A:HEA602 3.4 20.9 1.0
CHA A:HEA602 3.5 20.1 1.0
CHB A:HEA602 3.5 19.3 1.0
CHD A:HEA602 3.5 19.1 1.0
O2 A:PER608 3.6 23.2 0.5
O A:HOH859 4.1 23.2 0.4
ND1 A:HIS376 4.2 20.7 1.0
C3B A:HEA602 4.2 23.6 1.0
CG A:HIS376 4.2 21.2 1.0
C3A A:HEA602 4.2 22.7 1.0
C3D A:HEA602 4.2 24.5 1.0
C2B A:HEA602 4.3 22.4 1.0
C2A A:HEA602 4.3 20.4 1.0
C2C A:HEA602 4.3 20.2 1.0
C2D A:HEA602 4.3 22.8 1.0
C3C A:HEA602 4.3 18.5 1.0
CU A:CU603 4.8 22.5 1.0
CG1 A:VAL380 4.9 12.7 0.2
CG2 A:VAL243 4.9 22.6 1.0

Iron binding site 3 out of 4 in 7cp5

Go back to Iron Binding Sites List in 7cp5
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:24.1
occ:1.00
 FE N:HEA602 0.0 24.1 1.0
NE2 N:HIS378 2.0 24.4 1.0
NC N:HEA602 2.0 25.1 1.0
NE2 N:HIS61 2.0 21.8 1.0
NA N:HEA602 2.0 25.2 1.0
NB N:HEA602 2.0 24.5 1.0
ND N:HEA602 2.0 24.8 1.0
CE1 N:HIS378 2.9 27.6 1.0
CD2 N:HIS61 3.0 24.1 1.0
CE1 N:HIS61 3.0 27.8 1.0
C1B N:HEA602 3.0 24.4 1.0
C4B N:HEA602 3.0 25.7 1.0
C4A N:HEA602 3.0 28.7 1.0
C1D N:HEA602 3.0 23.2 1.0
C4C N:HEA602 3.0 25.5 1.0
C1A N:HEA602 3.0 26.8 1.0
C1C N:HEA602 3.1 24.5 1.0
CD2 N:HIS378 3.1 24.3 1.0
C4D N:HEA602 3.1 23.6 1.0
CHB N:HEA602 3.4 26.0 1.0
CHC N:HEA602 3.4 23.4 1.0
CHD N:HEA602 3.5 26.0 1.0
CHA N:HEA602 3.5 27.3 1.0
ND1 N:HIS378 4.1 26.7 1.0
ND1 N:HIS61 4.1 26.4 1.0
CG N:HIS61 4.1 24.3 1.0
CG N:HIS378 4.2 21.9 1.0
C3A N:HEA602 4.2 25.1 1.0
C2B N:HEA602 4.2 25.3 1.0
C3B N:HEA602 4.3 21.8 1.0
C2A N:HEA602 4.3 24.2 1.0
C2D N:HEA602 4.3 21.1 1.0
C3C N:HEA602 4.3 23.8 1.0
C2C N:HEA602 4.3 23.3 1.0
C3D N:HEA602 4.3 22.9 1.0
OG N:SER382 4.6 64.2 0.1
CE1 N:PHE377 4.8 24.1 1.0

Iron binding site 4 out of 4 in 7cp5

Go back to Iron Binding Sites List in 7cp5
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:23.6
occ:1.00
 FE N:HEA603 0.0 23.6 1.0
O N:HOH707 1.7 19.4 0.5
NB N:HEA603 2.0 23.8 1.0
NC N:HEA603 2.0 23.8 1.0
ND N:HEA603 2.0 24.1 1.0
NA N:HEA603 2.0 24.4 1.0
NE2 N:HIS376 2.1 23.4 1.0
O1 N:PER610 2.2 28.8 0.5
C1B N:HEA603 3.0 21.4 1.0
CE1 N:HIS376 3.0 25.7 1.0
C4B N:HEA603 3.0 21.5 1.0
C4C N:HEA603 3.0 20.0 1.0
C1D N:HEA603 3.0 22.1 1.0
C1A N:HEA603 3.1 29.0 1.0
C4A N:HEA603 3.1 21.6 1.0
C4D N:HEA603 3.1 26.5 1.0
C1C N:HEA603 3.1 23.1 1.0
CD2 N:HIS376 3.1 26.1 1.0
CHA N:HEA603 3.4 21.9 1.0
CHD N:HEA603 3.5 22.0 1.0
CHC N:HEA603 3.5 21.8 1.0
CHB N:HEA603 3.5 20.3 1.0
O2 N:PER610 3.6 28.9 0.5
O N:HOH884 4.0 20.2 0.4
ND1 N:HIS376 4.2 23.5 1.0
C2B N:HEA603 4.2 22.8 1.0
C3B N:HEA603 4.2 25.8 1.0
CG N:HIS376 4.2 24.6 1.0
C3A N:HEA603 4.2 24.1 1.0
C3D N:HEA603 4.3 24.4 1.0
C2A N:HEA603 4.3 23.6 1.0
C2D N:HEA603 4.3 23.2 1.0
C2C N:HEA603 4.3 21.1 1.0
C3C N:HEA603 4.3 20.7 1.0
CU N:CU604 4.8 24.3 1.0
CG1 N:VAL380 4.8 3.1 0.1
CG2 N:VAL243 4.9 24.5 1.0

Reference:

A.Shimada, F.Hara, K.Shinzawa-Itoh, N.Kanehisa, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. Critical Roles of the Cub Site in Efficient Proton Pumping As Revealed By Crystal Structures of Mammalian Cytochrome C Oxidase Catalytic Intermediates J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Thu Aug 8 03:14:07 2024

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