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Iron in PDB 7thu: Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays

Enzymatic activity of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays

All present enzymatic activity of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays:
1.9.3.1;

Protein crystallography data

The structure of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7thu was solved by I.Ishigami, D.L.Rousseau, S.-R.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.182, 182.282, 208.683, 90, 90, 90
R / Rfree (%) 18.4 / 21.3

Other elements in 7thu:

The structure of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays (pdb code 7thu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7thu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7thu

Go back to Iron Binding Sites List in 7thu
Iron binding site 1 out of 4 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:29.5
occ:1.00
 FE A:HEA606 0.0 29.5 1.0
ND A:HEA606 2.0 24.6 1.0
NB A:HEA606 2.0 30.0 1.0
NA A:HEA606 2.1 31.0 1.0
NC A:HEA606 2.1 29.0 1.0
NE2 A:HIS376 2.2 33.3 1.0
C1A A:HEA606 3.0 26.7 1.0
C4D A:HEA606 3.0 28.6 1.0
C1B A:HEA606 3.1 30.4 1.0
C4B A:HEA606 3.1 27.2 1.0
C1C A:HEA606 3.1 26.5 1.0
C4A A:HEA606 3.1 27.1 1.0
C1D A:HEA606 3.1 29.9 1.0
CE1 A:HIS376 3.1 34.1 1.0
C4C A:HEA606 3.2 26.7 1.0
CD2 A:HIS376 3.2 30.2 1.0
CHA A:HEA606 3.4 25.0 1.0
CHC A:HEA606 3.4 27.3 1.0
CHB A:HEA606 3.6 27.9 1.0
CHD A:HEA606 3.6 26.2 1.0
ND1 A:HIS376 4.2 30.4 1.0
C3D A:HEA606 4.3 27.1 1.0
C2B A:HEA606 4.3 26.3 1.0
CG A:HIS376 4.3 30.6 1.0
C2A A:HEA606 4.3 29.1 1.0
C3A A:HEA606 4.4 29.6 1.0
C2D A:HEA606 4.4 27.8 1.0
C3B A:HEA606 4.4 31.2 1.0
C2C A:HEA606 4.5 28.9 1.0
C3C A:HEA606 4.5 27.7 1.0
CG2 A:VAL380 4.7 40.1 1.0

Iron binding site 2 out of 4 in 7thu

Go back to Iron Binding Sites List in 7thu
Iron binding site 2 out of 4 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe607

b:28.2
occ:1.00
 FE A:HEA607 0.0 28.2 1.0
NE2 A:HIS61 2.0 23.7 1.0
NE2 A:HIS378 2.0 25.1 1.0
NB A:HEA607 2.0 29.3 1.0
ND A:HEA607 2.1 25.9 1.0
NA A:HEA607 2.1 30.6 1.0
NC A:HEA607 2.1 30.2 1.0
CE1 A:HIS378 2.9 30.4 1.0
CE1 A:HIS61 3.0 28.2 1.0
CD2 A:HIS61 3.0 26.6 1.0
C4A A:HEA607 3.0 28.4 1.0
CD2 A:HIS378 3.1 26.4 1.0
C1D A:HEA607 3.1 30.5 1.0
C4D A:HEA607 3.1 29.3 1.0
C1B A:HEA607 3.1 29.3 1.0
C1A A:HEA607 3.1 29.0 1.0
C4B A:HEA607 3.1 28.2 1.0
C4C A:HEA607 3.1 26.6 1.0
C1C A:HEA607 3.1 25.9 1.0
CHC A:HEA607 3.4 24.1 1.0
CHD A:HEA607 3.4 25.9 1.0
CHB A:HEA607 3.4 26.6 1.0
CHA A:HEA607 3.5 27.8 1.0
ND1 A:HIS61 4.1 25.1 1.0
ND1 A:HIS378 4.1 25.9 1.0
CG A:HIS61 4.1 24.4 1.0
CG A:HIS378 4.2 27.1 1.0
C3D A:HEA607 4.3 26.6 1.0
C2B A:HEA607 4.3 25.9 1.0
C3A A:HEA607 4.3 29.5 1.0
C3B A:HEA607 4.4 29.3 1.0
C2D A:HEA607 4.4 27.4 1.0
C2A A:HEA607 4.4 29.0 1.0
C3C A:HEA607 4.4 25.3 1.0
C2C A:HEA607 4.4 28.3 1.0
OG A:SER382 4.7 54.7 1.0

Iron binding site 3 out of 4 in 7thu

Go back to Iron Binding Sites List in 7thu
Iron binding site 3 out of 4 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe606

b:35.1
occ:1.00
 FE N:HEA606 0.0 35.1 1.0
NC N:HEA606 2.0 29.7 1.0
NA N:HEA606 2.1 34.9 1.0
NB N:HEA606 2.1 31.1 1.0
ND N:HEA606 2.1 30.3 1.0
NE2 N:HIS376 2.2 40.0 1.0
C1B N:HEA606 3.1 30.8 1.0
C4C N:HEA606 3.1 31.9 1.0
C1C N:HEA606 3.1 32.3 1.0
C1A N:HEA606 3.1 33.6 1.0
C4A N:HEA606 3.1 33.8 1.0
C4D N:HEA606 3.1 29.5 1.0
C1D N:HEA606 3.1 30.9 1.0
C4B N:HEA606 3.1 27.8 1.0
CD2 N:HIS376 3.2 39.1 1.0
CE1 N:HIS376 3.2 39.3 1.0
CHA N:HEA606 3.5 30.8 1.0
CHB N:HEA606 3.5 34.9 1.0
CHC N:HEA606 3.5 29.8 1.0
CHD N:HEA606 3.5 31.6 1.0
C2B N:HEA606 4.3 29.6 1.0
ND1 N:HIS376 4.3 37.5 1.0
CG N:HIS376 4.3 36.3 1.0
C3C N:HEA606 4.3 31.3 1.0
C3D N:HEA606 4.4 30.4 1.0
C3A N:HEA606 4.4 35.3 1.0
C2A N:HEA606 4.4 36.1 1.0
C2C N:HEA606 4.4 32.9 1.0
C3B N:HEA606 4.4 29.6 1.0
C2D N:HEA606 4.4 31.2 1.0
CG2 N:VAL380 4.7 41.1 1.0

Iron binding site 4 out of 4 in 7thu

Go back to Iron Binding Sites List in 7thu
Iron binding site 4 out of 4 in the Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Reduced Bovine Cytochrome C Oxidase at 1.93 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe607

b:35.9
occ:1.00
 FE N:HEA607 0.0 35.9 1.0
NE2 N:HIS61 2.0 35.0 1.0
NA N:HEA607 2.0 34.1 1.0
NC N:HEA607 2.0 34.4 1.0
NE2 N:HIS378 2.1 33.0 1.0
NB N:HEA607 2.1 36.0 1.0
ND N:HEA607 2.1 36.3 1.0
CD2 N:HIS61 3.0 35.3 1.0
C4A N:HEA607 3.0 36.3 1.0
C4C N:HEA607 3.0 37.1 1.0
C1B N:HEA607 3.1 33.6 1.0
CD2 N:HIS378 3.1 31.7 1.0
CE1 N:HIS61 3.1 37.4 1.0
CE1 N:HIS378 3.1 33.5 1.0
C1A N:HEA607 3.1 36.1 1.0
C1C N:HEA607 3.1 36.4 1.0
C1D N:HEA607 3.1 33.6 1.0
C4D N:HEA607 3.1 34.6 1.0
C4B N:HEA607 3.1 33.5 1.0
CHD N:HEA607 3.4 35.3 1.0
CHB N:HEA607 3.4 33.0 1.0
CHC N:HEA607 3.5 33.7 1.0
CHA N:HEA607 3.5 34.4 1.0
CG N:HIS61 4.1 36.1 1.0
ND1 N:HIS61 4.1 37.1 1.0
ND1 N:HIS378 4.2 32.7 1.0
CG N:HIS378 4.2 32.0 1.0
C3A N:HEA607 4.3 34.0 1.0
C2B N:HEA607 4.3 35.9 1.0
C3C N:HEA607 4.3 33.3 1.0
C2A N:HEA607 4.4 31.1 1.0
C3D N:HEA607 4.4 34.1 1.0
C2C N:HEA607 4.4 34.8 1.0
C2D N:HEA607 4.4 35.7 1.0
C3B N:HEA607 4.4 37.9 1.0
OG N:SER382 4.8 64.6 1.0

Reference:

I.Ishigami, S.Russi, A.Cohen, S.R.Yeh, D.L.Rousseau. Temperature-Dependent Structural Transition Following X-Ray-Induced Metal Center Reduction in Oxidized Cytochrome C Oxidase. J.Biol.Chem. V. 298 01799 2022.
ISSN: ESSN 1083-351X
PubMed: 35257742
DOI: 10.1016/J.JBC.2022.101799
Page generated: Wed Apr 5 05:14:28 2023

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