Atomistry » Sodium » PDB 7t3s-7u1r » 7tih
Atomistry »
  Sodium »
    PDB 7t3s-7u1r »
      7tih »

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

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

All present enzymatic activity of 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 Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tih 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) 39.34 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.037, 182.696, 205.854, 90, 90, 90
R / Rfree (%) 19.3 / 23.5

Other elements in 7tih:

The structure of Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Oxidized Bovine Cytochrome C Oxidase with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure (pdb code 7tih). 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 with Reduced Metal Centers Induced By Synchrotron X-Ray Exposure, PDB code: 7tih:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7tih

Go back to Sodium Binding Sites List in 7tih
Sodium binding site 1 out of 2 in the 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 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:Na603

b:30.4
occ:1.00
 OE1 A:GLU40 2.2 27.9 1.0
O A:HOH816 2.2 28.5 1.0
O A:SER441 2.3 34.6 1.0
O A:GLY45 2.3 33.2 1.0
O A:GLU40 2.3 35.5 1.0
CD A:GLU40 3.2 34.4 1.0
C A:GLU40 3.4 29.7 1.0
C A:GLY45 3.4 28.3 1.0
C A:SER441 3.5 32.9 1.0
CG A:GLU40 3.6 34.3 1.0
CB A:ASP442 3.9 31.1 1.0
CA A:ASP442 4.0 30.1 1.0
CA A:THR46 4.0 31.1 1.0
N A:THR46 4.0 27.1 1.0
OD1 A:ASP442 4.1 34.3 1.0
CG A:ASP442 4.1 32.5 1.0
O A:GLN43 4.1 36.5 1.0
N A:ASP442 4.2 29.4 1.0
CA A:GLU40 4.2 31.7 1.0
N A:LEU41 4.3 29.8 1.0
CA A:LEU41 4.4 31.2 1.0
OE2 A:GLU40 4.4 33.7 1.0
CB A:GLU40 4.4 31.9 1.0
N A:LEU47 4.5 39.2 1.0
N A:GLY45 4.5 31.4 1.0
CA A:GLY45 4.6 30.7 1.0
CA A:SER441 4.6 33.5 1.0
C A:THR46 4.6 37.0 1.0
CD2 A:LEU41 4.7 35.6 1.0
OD2 A:ASP442 4.9 34.5 1.0
CB A:SER441 5.0 32.5 1.0

Sodium binding site 2 out of 2 in 7tih

Go back to Sodium Binding Sites List in 7tih
Sodium binding site 2 out of 2 in the 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 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:Na603

b:32.0
occ:1.00
 OE1 N:GLU40 2.2 33.1 1.0
O N:HOH811 2.3 33.5 1.0
O N:GLU40 2.3 38.2 1.0
O N:SER441 2.3 36.9 1.0
O N:GLY45 2.3 40.0 1.0
CD N:GLU40 3.3 40.1 1.0
C N:GLU40 3.4 38.5 1.0
C N:GLY45 3.4 40.6 1.0
C N:SER441 3.4 35.3 1.0
CG N:GLU40 3.6 40.1 1.0
CA N:ASP442 3.9 37.7 1.0
CB N:ASP442 3.9 39.9 1.0
N N:THR46 4.1 40.3 1.0
CA N:THR46 4.1 41.1 1.0
N N:ASP442 4.1 34.5 1.0
O N:GLN43 4.1 38.6 1.0
OD1 N:ASP442 4.1 45.2 1.0
CG N:ASP442 4.2 43.1 1.0
CA N:GLU40 4.2 41.6 1.0
N N:LEU41 4.2 36.8 1.0
CA N:LEU41 4.4 37.0 1.0
OE2 N:GLU40 4.4 40.5 1.0
N N:GLY45 4.5 40.3 1.0
CB N:GLU40 4.5 43.0 1.0
CA N:GLY45 4.6 40.4 1.0
N N:LEU47 4.6 54.6 1.0
CA N:SER441 4.6 38.4 1.0
CD2 N:LEU41 4.7 41.9 1.0
C N:THR46 4.7 48.1 1.0
OD2 N:ASP442 4.9 41.5 1.0
CB N:SER441 5.0 37.9 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 09:06:26 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy