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Iron in PDB 7tih: Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure

Enzymatic activity of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure

All present enzymatic activity of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure:
1.9.3.1;

Protein crystallography data

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tih was solved by I.Ishigami, D.L.Rousseau, S.-R.Yeh, S.Russi, A.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.34 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.037, 182.696, 205.854, 90, 90, 90
R / Rfree (%) 19.3 / 23.5

Other elements in 7tih:

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure (pdb code 7tih). 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 with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tih:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7tih

Go back to Iron Binding Sites List in 7tih
Iron binding site 1 out of 4 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


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 with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:29.3
occ:1.00
 FE A:HEA606 0.0 29.3 1.0
O A:OH618 1.8 21.5 0.9
NB A:HEA606 2.1 26.7 1.0
ND A:HEA606 2.1 28.7 1.0
NA A:HEA606 2.1 28.0 1.0
NE2 A:HIS376 2.1 31.6 1.0
NC A:HEA606 2.1 31.3 1.0
CE1 A:HIS376 2.9 32.7 1.0
C1B A:HEA606 3.0 27.3 1.0
C4D A:HEA606 3.1 29.0 1.0
C4A A:HEA606 3.1 28.2 1.0
C4B A:HEA606 3.1 29.1 1.0
C1D A:HEA606 3.1 29.7 1.0
C1A A:HEA606 3.1 26.3 1.0
C4C A:HEA606 3.1 30.1 1.0
C1C A:HEA606 3.1 30.0 1.0
CD2 A:HIS376 3.2 33.6 1.0
O A:HOH701 3.3 17.4 0.8
CHB A:HEA606 3.4 29.0 1.0
CHA A:HEA606 3.4 26.5 1.0
CHD A:HEA606 3.5 28.7 1.0
CHC A:HEA606 3.5 28.9 1.0
ND1 A:HIS376 4.1 31.9 1.0
CG A:HIS376 4.3 33.2 1.0
C3D A:HEA606 4.4 29.9 1.0
C2B A:HEA606 4.4 27.9 1.0
C2D A:HEA606 4.4 29.8 1.0
C3A A:HEA606 4.4 28.2 1.0
C3B A:HEA606 4.4 28.9 1.0
C3C A:HEA606 4.4 31.6 1.0
C2A A:HEA606 4.4 28.2 1.0
C2C A:HEA606 4.4 30.7 1.0
CG2 A:VAL243 4.8 29.0 1.0
CU A:CU601 4.8 31.7 1.0

Iron binding site 2 out of 4 in 7tih

Go back to Iron Binding Sites List in 7tih
Iron binding site 2 out of 4 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


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 with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe607

b:28.9
occ:1.00
 FE A:HEA607 0.0 28.9 1.0
NE2 A:HIS61 2.0 27.2 1.0
NE2 A:HIS378 2.0 28.5 1.0
ND A:HEA607 2.1 29.6 1.0
NB A:HEA607 2.1 30.1 1.0
NC A:HEA607 2.1 32.8 1.0
NA A:HEA607 2.1 33.9 1.0
CD2 A:HIS61 2.9 26.4 1.0
CE1 A:HIS378 3.0 29.8 1.0
CE1 A:HIS61 3.0 28.4 1.0
CD2 A:HIS378 3.0 28.7 1.0
C1D A:HEA607 3.0 31.4 1.0
C1B A:HEA607 3.1 31.2 1.0
C4D A:HEA607 3.1 31.0 1.0
C4C A:HEA607 3.1 31.3 1.0
C1C A:HEA607 3.1 30.6 1.0
C4B A:HEA607 3.1 30.3 1.0
C4A A:HEA607 3.1 32.4 1.0
C1A A:HEA607 3.1 32.9 1.0
CHD A:HEA607 3.4 31.3 1.0
CHB A:HEA607 3.4 33.0 1.0
CHC A:HEA607 3.4 29.2 1.0
CHA A:HEA607 3.5 32.7 1.0
ND1 A:HIS378 4.1 31.1 1.0
ND1 A:HIS61 4.1 27.2 1.0
CG A:HIS61 4.1 26.3 1.0
CG A:HIS378 4.1 29.9 1.0
C2D A:HEA607 4.4 27.9 1.0
C3D A:HEA607 4.4 29.6 1.0
C3C A:HEA607 4.4 31.7 1.0
C2B A:HEA607 4.4 30.4 1.0
C3A A:HEA607 4.4 32.7 1.0
C2C A:HEA607 4.4 34.1 1.0
C2A A:HEA607 4.4 32.1 1.0
C3B A:HEA607 4.4 29.5 1.0
CE1 A:PHE377 4.9 32.6 1.0

Iron binding site 3 out of 4 in 7tih

Go back to Iron Binding Sites List in 7tih
Iron binding site 3 out of 4 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


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 with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe605

b:30.7
occ:1.00
 FE N:HEA605 0.0 30.7 1.0
O N:OH618 1.8 18.6 0.9
ND N:HEA605 2.0 30.9 1.0
NB N:HEA605 2.0 29.2 1.0
NA N:HEA605 2.1 30.8 1.0
NC N:HEA605 2.1 31.7 1.0
NE2 N:HIS376 2.1 41.1 1.0
C4D N:HEA605 3.0 31.0 1.0
C1B N:HEA605 3.0 31.1 1.0
C4A N:HEA605 3.1 33.6 1.0
C4B N:HEA605 3.1 30.6 1.0
C1A N:HEA605 3.1 30.1 1.0
C1D N:HEA605 3.1 31.5 1.0
C1C N:HEA605 3.1 32.0 1.0
C4C N:HEA605 3.1 33.7 1.0
CD2 N:HIS376 3.1 39.1 1.0
CE1 N:HIS376 3.1 42.7 1.0
O N:HOH701 3.4 23.2 0.8
CHA N:HEA605 3.4 31.9 1.0
CHB N:HEA605 3.4 31.4 1.0
CHC N:HEA605 3.5 30.8 1.0
CHD N:HEA605 3.5 31.1 1.0
ND1 N:HIS376 4.2 39.8 1.0
CG N:HIS376 4.3 37.8 1.0
C3D N:HEA605 4.3 30.5 1.0
C3A N:HEA605 4.4 33.0 1.0
C2D N:HEA605 4.4 29.0 1.0
C2B N:HEA605 4.4 29.9 1.0
C2A N:HEA605 4.4 32.1 1.0
C3B N:HEA605 4.4 30.0 1.0
C3C N:HEA605 4.4 33.7 1.0
C2C N:HEA605 4.4 34.7 1.0
CU N:CU601 4.8 33.7 1.0
CG2 N:VAL243 4.9 35.0 1.0

Iron binding site 4 out of 4 in 7tih

Go back to Iron Binding Sites List in 7tih
Iron binding site 4 out of 4 in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure


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 with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe606

b:34.0
occ:1.00
 FE N:HEA606 0.0 34.0 1.0
NE2 N:HIS61 2.0 31.9 1.0
NE2 N:HIS378 2.0 27.7 1.0
NA N:HEA606 2.1 35.9 1.0
NB N:HEA606 2.1 37.9 1.0
ND N:HEA606 2.1 36.8 1.0
NC N:HEA606 2.1 35.5 1.0
CD2 N:HIS61 2.9 31.6 1.0
CE1 N:HIS378 3.0 28.1 1.0
C4A N:HEA606 3.0 38.6 1.0
C1B N:HEA606 3.1 39.2 1.0
C4D N:HEA606 3.1 34.3 1.0
C1A N:HEA606 3.1 37.6 1.0
CD2 N:HIS378 3.1 27.4 1.0
CE1 N:HIS61 3.1 33.7 1.0
C1D N:HEA606 3.1 36.2 1.0
C4C N:HEA606 3.1 35.9 1.0
C1C N:HEA606 3.1 35.8 1.0
C4B N:HEA606 3.1 38.2 1.0
CHB N:HEA606 3.4 37.9 1.0
CHA N:HEA606 3.4 39.2 1.0
CHC N:HEA606 3.5 35.3 1.0
CHD N:HEA606 3.5 33.6 1.0
CG N:HIS61 4.1 33.6 1.0
ND1 N:HIS378 4.1 26.4 1.0
ND1 N:HIS61 4.1 33.2 1.0
CG N:HIS378 4.2 27.1 1.0
C3A N:HEA606 4.3 40.2 1.0
C3D N:HEA606 4.4 32.7 1.0
C2B N:HEA606 4.4 38.8 1.0
C2A N:HEA606 4.4 38.5 1.0
C2D N:HEA606 4.4 35.5 1.0
C3C N:HEA606 4.4 34.1 1.0
C3B N:HEA606 4.5 36.4 1.0
C2C N:HEA606 4.5 36.0 1.0
CE1 N:PHE377 4.9 36.6 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: Fri Aug 9 01:56:33 2024

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