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Iron in PDB 7tie: Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays

Enzymatic activity of Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays

All present enzymatic activity of Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays:
1.9.3.1;

Protein crystallography data

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7tie 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) 39.99 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.118, 182.415, 208.547, 90, 90, 90
R / Rfree (%) 18.5 / 21.5

Other elements in 7tie:

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays (pdb code 7tie). 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 Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays, PDB code: 7tie:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7tie

Go back to Iron Binding Sites List in 7tie
Iron binding site 1 out of 4 in the Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 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 Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:26.1
occ:1.00
 FE A:HEA605 0.0 26.1 1.0
NB A:HEA605 2.0 27.2 1.0
ND A:HEA605 2.0 25.7 1.0
O A:OH619 2.0 24.7 0.9
NC A:HEA605 2.1 26.8 1.0
NA A:HEA605 2.1 25.1 1.0
NE2 A:HIS376 2.2 28.8 1.0
C4B A:HEA605 3.0 25.5 1.0
C1A A:HEA605 3.0 23.0 1.0
C4D A:HEA605 3.0 24.8 1.0
C1C A:HEA605 3.0 25.9 1.0
C1B A:HEA605 3.1 27.0 1.0
C4A A:HEA605 3.1 24.3 1.0
C4C A:HEA605 3.1 24.7 1.0
C1D A:HEA605 3.1 26.6 1.0
CE1 A:HIS376 3.1 31.9 1.0
CD2 A:HIS376 3.2 27.3 1.0
CHC A:HEA605 3.4 23.8 1.0
CHA A:HEA605 3.4 22.2 1.0
CHB A:HEA605 3.5 25.1 1.0
CHD A:HEA605 3.5 22.0 1.0
O A:HOH701 3.8 25.5 0.6
ND1 A:HIS376 4.3 28.0 1.0
CG A:HIS376 4.3 27.0 1.0
C3A A:HEA605 4.3 26.5 1.0
C2A A:HEA605 4.3 26.2 1.0
C3D A:HEA605 4.3 25.1 1.0
C2B A:HEA605 4.3 24.2 1.0
C3C A:HEA605 4.4 24.2 1.0
C3B A:HEA605 4.4 26.4 1.0
C2D A:HEA605 4.4 23.9 1.0
C2C A:HEA605 4.4 26.1 1.0
CU A:CU601 4.9 28.6 1.0
CG2 A:VAL243 5.0 26.4 1.0

Iron binding site 2 out of 4 in 7tie

Go back to Iron Binding Sites List in 7tie
Iron binding site 2 out of 4 in the Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 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 Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:25.4
occ:1.00
 FE A:HEA606 0.0 25.4 1.0
NE2 A:HIS61 2.0 20.9 1.0
NE2 A:HIS378 2.0 21.4 1.0
ND A:HEA606 2.0 24.7 1.0
NB A:HEA606 2.0 26.5 1.0
NA A:HEA606 2.1 25.6 1.0
NC A:HEA606 2.1 27.5 1.0
CE1 A:HIS61 3.0 25.1 1.0
CE1 A:HIS378 3.0 26.3 1.0
C1B A:HEA606 3.0 25.2 1.0
C4A A:HEA606 3.0 25.9 1.0
CD2 A:HIS378 3.0 22.4 1.0
CD2 A:HIS61 3.0 24.1 1.0
C1D A:HEA606 3.0 28.2 1.0
C4D A:HEA606 3.0 26.2 1.0
C1A A:HEA606 3.1 25.1 1.0
C4B A:HEA606 3.1 26.4 1.0
C4C A:HEA606 3.1 23.7 1.0
C1C A:HEA606 3.1 24.9 1.0
CHB A:HEA606 3.3 23.4 1.0
CHC A:HEA606 3.4 23.1 1.0
CHD A:HEA606 3.4 25.5 1.0
CHA A:HEA606 3.4 24.4 1.0
ND1 A:HIS61 4.1 23.7 1.0
ND1 A:HIS378 4.1 24.0 1.0
CG A:HIS61 4.2 21.4 1.0
CG A:HIS378 4.2 25.5 1.0
C3A A:HEA606 4.3 27.2 1.0
C2B A:HEA606 4.3 24.8 1.0
C3D A:HEA606 4.3 25.5 1.0
C2D A:HEA606 4.3 25.8 1.0
C2A A:HEA606 4.4 26.7 1.0
C3B A:HEA606 4.4 25.8 1.0
C3C A:HEA606 4.4 20.8 1.0
C2C A:HEA606 4.4 22.7 1.0
CE1 A:PHE377 4.9 28.6 1.0

Iron binding site 3 out of 4 in 7tie

Go back to Iron Binding Sites List in 7tie
Iron binding site 3 out of 4 in the Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 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 Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe607

b:31.7
occ:1.00
 FE N:HEA607 0.0 31.7 1.0
NC N:HEA607 2.0 27.4 1.0
NA N:HEA607 2.0 29.6 1.0
NB N:HEA607 2.1 29.6 1.0
ND N:HEA607 2.1 28.4 1.0
O N:OH623 2.1 31.9 0.9
NE2 N:HIS376 2.2 35.0 1.0
C1C N:HEA607 3.0 29.3 1.0
C4C N:HEA607 3.0 30.0 1.0
C1A N:HEA607 3.0 29.9 1.0
C4A N:HEA607 3.0 30.7 1.0
C1B N:HEA607 3.1 26.4 1.0
C4D N:HEA607 3.1 26.7 1.0
C4B N:HEA607 3.1 25.4 1.0
C1D N:HEA607 3.1 28.3 1.0
CD2 N:HIS376 3.2 34.8 1.0
CE1 N:HIS376 3.2 37.7 1.0
CHB N:HEA607 3.4 28.2 1.0
CHA N:HEA607 3.4 26.6 1.0
CHC N:HEA607 3.5 26.2 1.0
CHD N:HEA607 3.5 28.3 1.0
O N:HOH701 3.7 37.4 0.6
C3C N:HEA607 4.3 27.7 1.0
C2C N:HEA607 4.3 28.2 1.0
C3A N:HEA607 4.3 30.2 1.0
C2A N:HEA607 4.3 30.8 1.0
ND1 N:HIS376 4.3 33.9 1.0
CG N:HIS376 4.3 33.1 1.0
C2B N:HEA607 4.4 26.5 1.0
C3B N:HEA607 4.4 25.9 1.0
C3D N:HEA607 4.4 29.1 1.0
C2D N:HEA607 4.5 25.9 1.0
CU N:CU601 4.9 34.1 1.0
CG2 N:VAL243 4.9 35.2 1.0

Iron binding site 4 out of 4 in 7tie

Go back to Iron Binding Sites List in 7tie
Iron binding site 4 out of 4 in the Structure of Oxidized Bovine Cytochrome C Oxidase at 1.90 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 Oxidized Bovine Cytochrome C Oxidase at 1.90 Angstrom Resolution Obtained By Synchrotron X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe608

b:33.1
occ:1.00
 FE N:HEA608 0.0 33.1 1.0
NA N:HEA608 2.0 32.1 1.0
NC N:HEA608 2.0 32.5 1.0
NB N:HEA608 2.1 33.8 1.0
NE2 N:HIS61 2.1 33.6 1.0
ND N:HEA608 2.1 36.1 1.0
NE2 N:HIS378 2.1 28.0 1.0
C4A N:HEA608 3.0 32.8 1.0
CD2 N:HIS61 3.0 31.1 1.0
C1B N:HEA608 3.0 33.3 1.0
C4C N:HEA608 3.0 31.8 1.0
C1A N:HEA608 3.0 34.6 1.0
CD2 N:HIS378 3.1 28.3 1.0
C1D N:HEA608 3.1 28.6 1.0
C1C N:HEA608 3.1 34.0 1.0
C4D N:HEA608 3.1 31.9 1.0
C4B N:HEA608 3.1 33.8 1.0
CE1 N:HIS378 3.2 30.0 1.0
CE1 N:HIS61 3.2 37.0 1.0
CHB N:HEA608 3.3 30.6 1.0
CHD N:HEA608 3.4 30.3 1.0
CHA N:HEA608 3.5 34.4 1.0
CHC N:HEA608 3.5 33.5 1.0
CG N:HIS61 4.2 33.8 1.0
CG N:HIS378 4.2 28.6 1.0
C3A N:HEA608 4.2 31.7 1.0
ND1 N:HIS61 4.2 34.0 1.0
ND1 N:HIS378 4.3 28.1 1.0
C2A N:HEA608 4.3 32.2 1.0
C3C N:HEA608 4.3 29.3 1.0
C2B N:HEA608 4.4 34.5 1.0
C2C N:HEA608 4.4 32.5 1.0
C2D N:HEA608 4.4 33.6 1.0
C3D N:HEA608 4.4 32.3 1.0
C3B N:HEA608 4.5 33.5 1.0
CE1 N:PHE377 4.9 33.4 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: Fri Aug 9 01:55:02 2024

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