Atomistry » Iron » PDB 7tc8-7tqf » 7tii
Atomistry »
  Iron »
    PDB 7tc8-7tqf »
      7tii »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy