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Sodium 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
Iron (Fe) 4 atoms
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7thu

Go back to Sodium Binding Sites List in 7thu
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na603

b:35.9
occ:1.00
OE1 A:GLU40 2.2 35.4 1.0
O A:HOH852 2.2 30.9 1.0
O A:GLY45 2.3 42.6 1.0
O A:GLU40 2.3 32.0 1.0
O A:SER441 2.3 34.3 1.0
CD A:GLU40 3.2 36.7 1.0
C A:GLU40 3.3 32.0 1.0
O A:HOH739 3.4 44.8 1.0
CG A:GLU40 3.5 31.5 1.0
C A:GLY45 3.5 37.9 1.0
C A:SER441 3.5 32.1 1.0
O A:HOH858 3.8 40.3 1.0
O A:GLN43 4.0 34.3 1.0
CB A:ASP442 4.0 35.0 1.0
CA A:THR46 4.0 42.3 1.0
CA A:ASP442 4.1 33.7 1.0
CA A:GLU40 4.2 28.8 1.0
N A:THR46 4.2 36.0 1.0
CG A:ASP442 4.2 36.2 1.0
N A:LEU41 4.2 29.7 1.0
OD2 A:ASP442 4.3 34.1 1.0
N A:ASP442 4.3 34.6 1.0
OE2 A:GLU40 4.3 40.1 1.0
CA A:LEU41 4.3 29.4 1.0
CB A:GLU40 4.4 31.5 1.0
N A:LEU47 4.5 40.2 1.0
N A:GLY45 4.5 33.8 1.0
CD2 A:LEU41 4.6 32.5 1.0
C A:THR46 4.6 42.0 1.0
CA A:GLY45 4.6 33.7 1.0
CA A:SER441 4.7 33.6 1.0
OD1 A:ASP442 4.8 34.6 1.0

Sodium binding site 2 out of 2 in 7thu

Go back to Sodium Binding Sites List in 7thu
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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
N:Na603

b:49.5
occ:1.00
O N:HOH819 2.2 43.8 1.0
OE1 N:GLU40 2.3 44.9 1.0
O N:GLY45 2.3 62.4 1.0
O N:GLU40 2.3 40.2 1.0
O N:SER441 2.3 48.9 1.0
CD N:GLU40 3.2 48.2 1.0
O N:HOH704 3.2 53.5 1.0
C N:GLU40 3.4 38.2 1.0
CG N:GLU40 3.5 44.2 1.0
C N:GLY45 3.5 52.4 1.0
C N:SER441 3.5 38.8 1.0
O N:HOH870 3.8 54.0 1.0
O N:GLN43 3.9 42.3 1.0
CA N:ASP442 4.0 41.0 1.0
OD2 N:ASP442 4.0 40.3 1.0
CB N:ASP442 4.0 43.1 1.0
CA N:THR46 4.1 58.0 1.0
CG N:ASP442 4.1 41.1 1.0
N N:ASP442 4.2 41.1 1.0
N N:THR46 4.2 49.3 1.0
CA N:GLU40 4.3 36.2 1.0
N N:LEU41 4.3 39.0 1.0
OE2 N:GLU40 4.3 43.2 1.0
CA N:LEU41 4.4 40.0 1.0
CB N:GLU40 4.5 39.9 1.0
N N:GLY45 4.5 43.9 1.0
CA N:GLY45 4.6 44.3 1.0
N N:LEU47 4.6 51.9 1.0
CD2 N:LEU41 4.6 41.7 1.0
CA N:SER441 4.7 42.5 1.0
OD1 N:ASP442 4.7 41.0 1.0
C N:THR46 4.7 52.5 1.0
O N:HOH708 5.0 47.1 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 Apr 7 16:30:35 2023

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