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

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

All present enzymatic activity of Annealed 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 Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tii 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) 39.30 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.037, 182.633, 205.453, 90, 90, 90
R / Rfree (%) 20.6 / 25.3

Other elements in 7tii:

The structure of Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure 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 Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure (pdb code 7tii). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Annealed Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tii:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7tii

Go back to Iron Binding Sites List in 7tii
Iron binding site 1 out of 4 in the Annealed 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 Annealed 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:Fe601

b:31.4
occ:1.00
 FE A:HEA601 0.0 31.4 1.0
NE2 A:HIS378 2.0 28.4 1.0
NE2 A:HIS61 2.0 25.1 1.0
ND A:HEA601 2.1 33.1 1.0
NB A:HEA601 2.1 31.9 1.0
NC A:HEA601 2.1 36.2 1.0
NA A:HEA601 2.1 37.2 1.0
CE1 A:HIS378 2.9 28.5 1.0
CD2 A:HIS61 3.0 25.0 1.0
CD2 A:HIS378 3.0 29.5 1.0
C4B A:HEA601 3.1 34.0 1.0
C4D A:HEA601 3.1 32.6 1.0
CE1 A:HIS61 3.1 26.8 1.0
C1D A:HEA601 3.1 34.9 1.0
C1B A:HEA601 3.1 35.4 1.0
C4C A:HEA601 3.1 35.6 1.0
C4A A:HEA601 3.1 34.4 1.0
C1C A:HEA601 3.1 33.6 1.0
C1A A:HEA601 3.1 35.7 1.0
CHC A:HEA601 3.4 34.4 1.0
CHD A:HEA601 3.4 36.5 1.0
CHB A:HEA601 3.5 35.8 1.0
CHA A:HEA601 3.5 35.1 1.0
ND1 A:HIS378 4.0 30.9 1.0
CG A:HIS378 4.1 29.5 1.0
CG A:HIS61 4.2 26.1 1.0
ND1 A:HIS61 4.2 27.6 1.0
C3D A:HEA601 4.4 33.7 1.0
C3B A:HEA601 4.4 35.7 1.0
C2D A:HEA601 4.4 31.7 1.0
C3C A:HEA601 4.4 35.2 1.0
C2B A:HEA601 4.4 36.1 1.0
C3A A:HEA601 4.4 34.2 1.0
C2C A:HEA601 4.4 37.5 1.0
C2A A:HEA601 4.5 34.9 1.0
OG A:SER382 4.6 37.7 0.5
CE1 A:PHE377 5.0 40.2 1.0

Iron binding site 2 out of 4 in 7tii

Go back to Iron Binding Sites List in 7tii
Iron binding site 2 out of 4 in the Annealed 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 Annealed 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:Fe602

b:32.0
occ:1.00
 FE A:HEA602 0.0 32.0 1.0
ND A:HEA602 2.0 29.8 1.0
NB A:HEA602 2.1 30.3 1.0
O A:OH610 2.1 27.0 0.6
NA A:HEA602 2.1 29.8 1.0
NC A:HEA602 2.1 34.6 1.0
NE2 A:HIS376 2.2 37.5 1.0
C4D A:HEA602 3.0 30.6 1.0
C1B A:HEA602 3.1 31.5 1.0
C1D A:HEA602 3.1 30.3 1.0
C4A A:HEA602 3.1 30.0 1.0
C1A A:HEA602 3.1 27.4 1.0
C4B A:HEA602 3.1 33.2 1.0
CE1 A:HIS376 3.1 38.9 1.0
C1C A:HEA602 3.1 33.5 1.0
C4C A:HEA602 3.1 32.7 1.0
CD2 A:HIS376 3.3 37.4 1.0
O A:HOH701 3.4 8.1 0.3
CHA A:HEA602 3.4 27.8 1.0
CHB A:HEA602 3.4 32.7 1.0
CHC A:HEA602 3.5 34.1 1.0
CHD A:HEA602 3.5 29.8 1.0
ND1 A:HIS376 4.3 34.8 1.0
C3D A:HEA602 4.3 29.9 1.0
C2D A:HEA602 4.4 31.8 1.0
C3A A:HEA602 4.4 28.9 1.0
C3B A:HEA602 4.4 34.3 1.0
C3C A:HEA602 4.4 33.8 1.0
C2B A:HEA602 4.4 31.2 1.0
CG A:HIS376 4.4 34.7 1.0
C2A A:HEA602 4.4 29.3 1.0
C2C A:HEA602 4.4 34.2 1.0
CU A:CU603 4.9 32.3 1.0
CG1 A:VAL380 4.9 29.8 0.5

Iron binding site 3 out of 4 in 7tii

Go back to Iron Binding Sites List in 7tii
Iron binding site 3 out of 4 in the Annealed 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 Annealed 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:Fe601

b:35.6
occ:1.00
 FE N:HEA601 0.0 35.6 1.0
NE2 N:HIS61 2.0 33.0 1.0
NA N:HEA601 2.1 37.6 1.0
NE2 N:HIS378 2.1 30.0 1.0
NC N:HEA601 2.1 39.3 1.0
NB N:HEA601 2.1 42.8 1.0
ND N:HEA601 2.1 37.4 1.0
CD2 N:HIS61 2.9 33.6 1.0
CE1 N:HIS378 2.9 30.6 1.0
C4A N:HEA601 3.1 39.5 1.0
C4C N:HEA601 3.1 39.4 1.0
C4D N:HEA601 3.1 34.4 1.0
C4B N:HEA601 3.1 43.3 1.0
C1A N:HEA601 3.1 37.0 1.0
CE1 N:HIS61 3.1 33.3 1.0
C1D N:HEA601 3.1 36.0 1.0
C1B N:HEA601 3.1 40.5 1.0
C1C N:HEA601 3.1 39.5 1.0
CD2 N:HIS378 3.2 29.4 1.0
CHA N:HEA601 3.4 36.6 1.0
CHC N:HEA601 3.5 40.8 1.0
CHB N:HEA601 3.5 37.5 1.0
CHD N:HEA601 3.5 36.6 1.0
CG N:HIS61 4.1 34.1 1.0
ND1 N:HIS378 4.1 29.9 1.0
ND1 N:HIS61 4.2 32.4 1.0
CG N:HIS378 4.2 30.3 1.0
C3A N:HEA601 4.4 41.2 1.0
C3D N:HEA601 4.4 32.5 1.0
C3C N:HEA601 4.4 37.9 1.0
C3B N:HEA601 4.4 44.7 1.0
C2B N:HEA601 4.4 42.3 1.0
C2D N:HEA601 4.4 34.5 1.0
C2A N:HEA601 4.4 37.6 1.0
C2C N:HEA601 4.5 39.0 1.0
OG N:SER382 4.8 37.4 0.5
CE1 N:PHE377 4.9 36.0 1.0

Iron binding site 4 out of 4 in 7tii

Go back to Iron Binding Sites List in 7tii
Iron binding site 4 out of 4 in the Annealed 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 Annealed 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:Fe602

b:33.9
occ:1.00
 FE N:HEA602 0.0 33.9 1.0
ND N:HEA602 2.1 31.2 1.0
NB N:HEA602 2.1 31.3 1.0
NA N:HEA602 2.1 33.7 1.0
NC N:HEA602 2.1 33.6 1.0
O N:OH608 2.2 27.4 0.6
NE2 N:HIS376 2.2 42.3 1.0
C4D N:HEA602 3.0 31.2 1.0
C4B N:HEA602 3.1 32.9 1.0
C1A N:HEA602 3.1 33.4 1.0
C4C N:HEA602 3.1 35.0 1.0
C1B N:HEA602 3.1 34.0 1.0
C1D N:HEA602 3.1 31.9 1.0
C1C N:HEA602 3.1 33.3 1.0
C4A N:HEA602 3.1 36.6 1.0
CE1 N:HIS376 3.1 47.3 1.0
O N:HOH701 3.3 17.6 0.3
CD2 N:HIS376 3.3 41.8 1.0
CHA N:HEA602 3.4 33.0 1.0
CHC N:HEA602 3.4 33.4 1.0
CHD N:HEA602 3.5 32.7 1.0
CHB N:HEA602 3.5 34.7 1.0
ND1 N:HIS376 4.3 43.4 1.0
C3D N:HEA602 4.4 31.5 1.0
CG N:HIS376 4.4 40.2 1.0
C2D N:HEA602 4.4 30.1 1.0
C3C N:HEA602 4.4 36.8 1.0
C3A N:HEA602 4.4 35.4 1.0
C3B N:HEA602 4.4 33.1 1.0
C2B N:HEA602 4.4 32.8 1.0
C2C N:HEA602 4.4 36.0 1.0
C2A N:HEA602 4.4 34.2 1.0
CG1 N:VAL380 4.8 37.1 0.5
CU N:CU603 4.8 36.8 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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