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Iron in PDB 7d5x: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x 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) 39.70 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.767, 203.304, 177.566, 90, 90, 90
R / Rfree (%) 15.6 / 18.4

Other elements in 7d5x:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution (pdb code 7d5x). 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, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7d5x

Go back to Iron Binding Sites List in 7d5x
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:22.0
occ:1.00
 FE A:HEA601 0.0 22.0 1.0
NE2 A:HIS61 2.0 22.5 1.0
NE2 A:HIS378 2.0 20.6 1.0
NB A:HEA601 2.0 22.6 1.0
NC A:HEA601 2.0 20.9 1.0
ND A:HEA601 2.0 23.1 1.0
NA A:HEA601 2.0 21.3 1.0
CE1 A:HIS378 2.9 23.4 1.0
CE1 A:HIS61 2.9 24.8 1.0
C1C A:HEA601 3.0 22.5 1.0
CD2 A:HIS61 3.0 24.3 1.0
C4C A:HEA601 3.0 20.3 1.0
C4A A:HEA601 3.0 21.2 1.0
C1D A:HEA601 3.0 20.1 1.0
CD2 A:HIS378 3.0 24.3 1.0
C4B A:HEA601 3.0 21.1 1.0
C4D A:HEA601 3.0 23.5 1.0
C1B A:HEA601 3.1 20.4 1.0
C1A A:HEA601 3.1 20.8 1.0
CHC A:HEA601 3.4 17.8 1.0
CHB A:HEA601 3.4 21.4 1.0
CHD A:HEA601 3.5 17.7 1.0
CHA A:HEA601 3.5 20.5 1.0
ND1 A:HIS378 4.1 22.6 1.0
ND1 A:HIS61 4.1 24.7 1.0
CG A:HIS61 4.1 25.1 1.0
CG A:HIS378 4.1 24.0 1.0
C3A A:HEA601 4.2 23.3 1.0
C2C A:HEA601 4.2 21.3 1.0
C3C A:HEA601 4.2 18.5 1.0
C2D A:HEA601 4.2 20.2 1.0
C3D A:HEA601 4.3 20.4 1.0
C2A A:HEA601 4.3 20.7 1.0
C3B A:HEA601 4.3 20.8 1.0
C2B A:HEA601 4.3 23.4 1.0
OG A:SER382 4.6 28.1 0.6
CE1 A:PHE377 5.0 22.1 1.0

Iron binding site 2 out of 4 in 7d5x

Go back to Iron Binding Sites List in 7d5x
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:23.1
occ:1.00
 FE A:HEA602 0.0 23.1 1.0
O1 A:OXY607 1.9 14.7 0.2
NB A:HEA602 2.0 26.0 1.0
ND A:HEA602 2.0 24.2 1.0
NA A:HEA602 2.0 21.8 1.0
NC A:HEA602 2.1 21.7 1.0
NE2 A:HIS376 2.1 23.7 1.0
O2 A:OXY607 2.9 30.0 0.2
C4D A:HEA602 3.0 22.7 1.0
C4B A:HEA602 3.0 24.0 1.0
C4A A:HEA602 3.0 21.5 1.0
C1B A:HEA602 3.1 21.0 1.0
C4C A:HEA602 3.1 19.7 1.0
C1A A:HEA602 3.1 20.9 1.0
C1D A:HEA602 3.1 22.3 1.0
C1C A:HEA602 3.1 24.8 1.0
CE1 A:HIS376 3.1 26.2 1.0
CD2 A:HIS376 3.1 20.4 1.0
CHA A:HEA602 3.4 20.9 1.0
CHC A:HEA602 3.5 23.6 1.0
CHB A:HEA602 3.5 20.5 1.0
CHD A:HEA602 3.6 22.3 1.0
C3D A:HEA602 4.2 22.6 1.0
C3B A:HEA602 4.2 25.4 1.0
ND1 A:HIS376 4.3 24.1 1.0
C3A A:HEA602 4.3 24.1 1.0
C2B A:HEA602 4.3 22.9 1.0
C2A A:HEA602 4.3 20.8 1.0
CG A:HIS376 4.3 23.8 1.0
C2D A:HEA602 4.3 20.6 1.0
C3C A:HEA602 4.3 19.9 1.0
C2C A:HEA602 4.3 25.9 1.0
CG1 A:VAL380 4.6 20.1 0.6

Iron binding site 3 out of 4 in 7d5x

Go back to Iron Binding Sites List in 7d5x
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:24.9
occ:1.00
 FE N:HEA601 0.0 24.9 1.0
NE2 N:HIS378 2.0 25.2 1.0
NC N:HEA601 2.0 25.1 1.0
NE2 N:HIS61 2.0 25.6 1.0
NB N:HEA601 2.0 26.1 1.0
NA N:HEA601 2.0 24.2 1.0
ND N:HEA601 2.0 25.5 1.0
CE1 N:HIS378 3.0 31.7 1.0
CD2 N:HIS61 3.0 24.8 1.0
C1B N:HEA601 3.0 28.6 1.0
C1A N:HEA601 3.0 24.6 1.0
CE1 N:HIS61 3.0 28.5 1.0
C4B N:HEA601 3.0 28.1 1.0
CD2 N:HIS378 3.0 25.4 1.0
C1D N:HEA601 3.0 23.8 1.0
C1C N:HEA601 3.0 26.1 1.0
C4A N:HEA601 3.1 27.4 1.0
C4C N:HEA601 3.1 24.6 1.0
C4D N:HEA601 3.1 25.2 1.0
CHB N:HEA601 3.4 26.6 1.0
CHD N:HEA601 3.4 24.5 1.0
CHA N:HEA601 3.5 27.4 1.0
CHC N:HEA601 3.5 25.3 1.0
ND1 N:HIS378 4.1 26.5 1.0
ND1 N:HIS61 4.1 26.4 1.0
CG N:HIS61 4.1 25.1 1.0
CG N:HIS378 4.1 23.7 1.0
C2A N:HEA601 4.2 24.4 1.0
C3A N:HEA601 4.2 26.2 1.0
C3B N:HEA601 4.2 22.9 1.0
C2B N:HEA601 4.2 27.9 1.0
C2C N:HEA601 4.3 24.8 1.0
C3C N:HEA601 4.3 25.4 1.0
C2D N:HEA601 4.3 23.1 1.0
C3D N:HEA601 4.3 24.0 1.0
OG N:SER382 4.6 32.2 0.6
CE1 N:PHE377 4.9 24.6 1.0

Iron binding site 4 out of 4 in 7d5x

Go back to Iron Binding Sites List in 7d5x
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:24.6
occ:1.00
 FE N:HEA602 0.0 24.6 1.0
O1 N:OXY609 1.9 16.3 0.2
NB N:HEA602 2.0 24.5 1.0
ND N:HEA602 2.0 23.8 1.0
NC N:HEA602 2.0 23.6 1.0
NA N:HEA602 2.0 24.1 1.0
NE2 N:HIS376 2.1 25.9 1.0
O2 N:OXY609 2.9 25.1 0.2
C4D N:HEA602 3.0 24.0 1.0
C1A N:HEA602 3.0 26.2 1.0
C4B N:HEA602 3.0 24.0 1.0
C4A N:HEA602 3.0 21.2 1.0
C4C N:HEA602 3.0 22.9 1.0
C1B N:HEA602 3.0 23.6 1.0
CE1 N:HIS376 3.1 27.0 1.0
C1D N:HEA602 3.1 21.9 1.0
C1C N:HEA602 3.1 23.8 1.0
CD2 N:HIS376 3.2 25.7 1.0
CHA N:HEA602 3.4 22.5 1.0
CHB N:HEA602 3.5 23.2 1.0
CHC N:HEA602 3.5 25.7 1.0
CHD N:HEA602 3.5 22.4 1.0
C3A N:HEA602 4.2 24.7 1.0
ND1 N:HIS376 4.2 27.5 1.0
C2A N:HEA602 4.2 23.2 1.0
C3D N:HEA602 4.2 24.0 1.0
C3B N:HEA602 4.2 24.1 1.0
C2B N:HEA602 4.3 25.8 1.0
CG N:HIS376 4.3 25.5 1.0
C2D N:HEA602 4.3 24.1 1.0
C2C N:HEA602 4.3 23.9 1.0
C3C N:HEA602 4.3 22.8 1.0
CG1 N:VAL380 4.6 22.7 0.6
CG2 N:VAL243 4.9 23.6 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: Wed Aug 6 21:34:22 2025

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