Sodium 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
Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 7tie

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

b:25.7
occ:1.00
 O A:HOH847 2.2 25.8 1.0
OE1 A:GLU40 2.2 28.0 1.0
O A:SER441 2.3 28.2 1.0
O A:GLY45 2.3 32.1 1.0
O A:GLU40 2.3 27.7 1.0
CD A:GLU40 3.2 30.3 1.0
O A:HOH706 3.3 38.8 1.0
C A:GLU40 3.4 29.4 1.0
CG A:GLU40 3.5 27.3 1.0
C A:GLY45 3.5 29.9 1.0
C A:SER441 3.5 25.6 1.0
O A:GLN43 4.0 29.2 1.0
CB A:ASP442 4.1 28.5 1.0
CA A:ASP442 4.1 29.1 1.0
CA A:THR46 4.1 32.2 1.0
CA A:GLU40 4.1 27.6 1.0
N A:THR46 4.2 28.1 1.0
OD1 A:ASP442 4.2 28.1 1.0
N A:LEU41 4.2 25.2 1.0
N A:ASP442 4.2 29.3 1.0
CG A:ASP442 4.2 30.7 1.0
N A:LEU47 4.3 33.6 1.0
OE2 A:GLU40 4.3 30.9 1.0
CA A:LEU41 4.4 25.0 1.0
CB A:GLU40 4.4 29.2 1.0
N A:GLY45 4.5 29.4 1.0
CA A:SER441 4.6 28.5 1.0
CA A:GLY45 4.6 27.5 1.0
C A:THR46 4.6 35.7 1.0
CD2 A:LEU41 4.7 27.5 1.0
CB A:SER441 4.9 30.8 1.0
OD2 A:ASP442 5.0 30.2 1.0

Sodium binding site 2 out of 2 in 7tie

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

b:40.6
occ:1.00
 OE1 N:GLU40 2.2 38.5 1.0
O N:GLY45 2.2 49.2 1.0
O N:GLU40 2.3 37.9 1.0
O N:HOH840 2.3 35.6 1.0
O N:SER441 2.3 42.7 1.0
CD N:GLU40 3.2 41.6 1.0
O N:HOH739 3.3 45.5 1.0
C N:GLU40 3.4 34.7 1.0
C N:GLY45 3.4 44.2 1.0
CG N:GLU40 3.5 36.6 1.0
C N:SER441 3.5 34.1 1.0
O N:GLN43 4.0 41.8 1.0
CA N:ASP442 4.1 37.8 1.0
CA N:THR46 4.1 45.3 1.0
CB N:ASP442 4.1 40.6 1.0
OD1 N:ASP442 4.1 38.3 1.0
N N:THR46 4.2 42.7 1.0
CA N:GLU40 4.2 33.5 1.0
N N:ASP442 4.2 38.5 1.0
CG N:ASP442 4.3 40.2 1.0
N N:LEU41 4.3 35.1 1.0
CA N:LEU41 4.4 39.0 1.0
OE2 N:GLU40 4.4 40.4 1.0
CB N:GLU40 4.4 33.8 1.0
N N:GLY45 4.4 38.7 1.0
N N:LEU47 4.5 44.6 1.0
CA N:GLY45 4.5 39.0 1.0
CA N:SER441 4.6 36.8 1.0
CD2 N:LEU41 4.7 41.8 1.0
C N:THR46 4.7 45.6 1.0
CB N:SER441 4.9 36.5 1.0
OD2 N:ASP442 5.0 39.4 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: Wed Oct 9 09:06:24 2024

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