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

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 7tii

Go back to Sodium Binding Sites List in 7tii
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na605

b:33.0
occ:1.00
 O A:HOH778 2.2 25.2 1.0
O A:SER441 2.3 34.0 1.0
OE1 A:GLU40 2.3 32.4 1.0
O A:GLY45 2.3 34.7 1.0
O A:GLU40 2.3 35.0 1.0
CD A:GLU40 3.3 33.1 1.0
C A:GLU40 3.4 30.4 1.0
C A:GLY45 3.4 30.6 1.0
C A:SER441 3.5 32.2 1.0
CG A:GLU40 3.7 34.8 1.0
CA A:ASP442 3.9 30.7 1.0
CB A:ASP442 3.9 32.0 1.0
CA A:THR46 4.0 36.9 1.0
OD1 A:ASP442 4.0 29.4 1.0
O A:GLN43 4.1 37.9 1.0
N A:THR46 4.1 31.9 1.0
N A:ASP442 4.1 29.4 1.0
CG A:ASP442 4.1 33.8 1.0
CA A:GLU40 4.2 31.4 1.0
N A:LEU41 4.3 31.9 1.0
CA A:LEU41 4.4 34.1 1.0
N A:GLY45 4.4 30.7 1.0
OE2 A:GLU40 4.4 35.8 1.0
N A:LEU47 4.5 46.7 1.0
CA A:GLY45 4.5 31.2 1.0
CB A:GLU40 4.5 31.4 1.0
CD2 A:LEU41 4.6 43.0 1.0
CA A:SER441 4.6 35.1 1.0
C A:THR46 4.7 43.7 1.0
OD2 A:ASP442 4.9 34.9 1.0
CB A:SER441 5.0 34.6 1.0

Sodium binding site 2 out of 2 in 7tii

Go back to Sodium Binding Sites List in 7tii
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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
N:Na605

b:35.5
occ:1.00
 OE1 N:GLU40 2.3 33.4 1.0
O N:SER441 2.3 38.9 1.0
O N:GLY45 2.3 40.1 1.0
O N:GLU40 2.3 36.1 1.0
O N:HOH783 2.3 37.5 1.0
CD N:GLU40 3.2 35.9 1.0
C N:GLU40 3.4 38.5 1.0
C N:GLY45 3.4 39.6 1.0
C N:SER441 3.5 38.4 1.0
CG N:GLU40 3.5 37.2 1.0
CA N:THR46 3.9 45.1 1.0
CB N:ASP442 4.0 46.7 1.0
N N:THR46 4.0 40.6 1.0
CA N:ASP442 4.0 43.1 1.0
O N:GLN43 4.1 37.7 1.0
N N:ASP442 4.2 40.1 1.0
CA N:GLU40 4.2 39.7 1.0
CG N:ASP442 4.3 46.7 1.0
N N:LEU41 4.3 37.3 1.0
OE2 N:GLU40 4.4 35.9 1.0
N N:LEU47 4.4 56.0 1.0
CA N:LEU41 4.4 38.2 1.0
CB N:GLU40 4.5 38.5 1.0
OD1 N:ASP442 4.5 49.2 1.0
N N:GLY45 4.5 37.7 1.0
CA N:GLY45 4.5 38.7 1.0
CA N:SER441 4.6 38.7 1.0
C N:THR46 4.6 52.2 1.0
CD2 N:LEU41 4.8 40.4 1.0
OD2 N:ASP442 4.8 46.0 1.0
CB N:SER441 4.9 40.6 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: Wed Oct 9 09:06:34 2024

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