Atomistry » Sodium » PDB 5b05-5bom » 5b3s
Atomistry »
  Sodium »
    PDB 5b05-5bom »
      5b3s »

Sodium in PDB 5b3s: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s was solved by J.Baba, A.Shimada, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.491, 203.303, 177.484, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.4

Other elements in 5b3s:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) (pdb code 5b3s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5b3s

Go back to Sodium Binding Sites List in 5b3s
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:26.9
occ:1.00
O A:SER441 2.3 26.7 1.0
OE1 A:GLU40 2.3 26.9 1.0
O A:GLY45 2.3 29.6 1.0
O A:HOH836 2.3 28.5 1.0
O A:GLU40 2.3 26.5 1.0
CD A:GLU40 3.2 28.6 1.0
C A:GLU40 3.4 24.2 1.0
O A:HOH762 3.4 36.6 1.0
CG A:GLU40 3.5 27.1 1.0
C A:SER441 3.5 25.9 1.0
C A:GLY45 3.5 28.5 1.0
CB A:ASP442 3.9 24.4 1.0
CA A:ASP442 4.0 26.8 1.0
O A:GLN43 4.0 28.8 1.0
CA A:THR46 4.0 27.5 1.0
OD1 A:ASP442 4.2 28.8 1.0
CG A:ASP442 4.2 28.2 1.0
CA A:GLU40 4.2 25.1 1.0
N A:ASP442 4.2 26.1 1.0
N A:THR46 4.2 31.3 1.0
N A:LEU41 4.3 24.9 1.0
N A:LEU47 4.3 29.4 1.0
CA A:LEU41 4.4 25.4 1.0
OE2 A:GLU40 4.4 30.8 1.0
CB A:GLU40 4.4 26.1 1.0
N A:GLY45 4.4 29.4 1.0
C A:THR46 4.6 30.1 1.0
CA A:GLY45 4.6 29.6 1.0
CA A:SER441 4.7 26.1 1.0
CD2 A:LEU41 4.7 26.6 1.0
OD2 A:ASP442 4.9 29.3 1.0
CB A:SER441 5.0 26.6 1.0

Sodium binding site 2 out of 2 in 5b3s

Go back to Sodium Binding Sites List in 5b3s
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:31.7
occ:1.00
O N:SER441 2.3 30.4 1.0
OE1 N:GLU40 2.3 32.1 1.0
O N:GLY45 2.3 32.8 1.0
O N:GLU40 2.3 29.8 1.0
O N:HOH870 2.3 30.4 1.0
CD N:GLU40 3.2 35.3 1.0
C N:GLU40 3.3 28.2 1.0
O N:HOH804 3.4 37.6 1.0
C N:SER441 3.5 29.0 1.0
CG N:GLU40 3.5 30.7 1.0
C N:GLY45 3.5 36.3 1.0
CA N:ASP442 4.0 28.3 1.0
O N:GLN43 4.0 34.1 1.0
CA N:THR46 4.1 35.3 1.0
CB N:ASP442 4.1 30.8 1.0
OD1 N:ASP442 4.2 32.1 1.0
CG N:ASP442 4.2 33.0 1.0
CA N:GLU40 4.2 30.1 1.0
N N:ASP442 4.2 29.7 1.0
N N:LEU41 4.2 30.7 1.0
N N:THR46 4.3 33.5 1.0
CA N:LEU41 4.4 32.0 1.0
N N:LEU47 4.4 39.2 1.0
OE2 N:GLU40 4.4 33.8 1.0
CB N:GLU40 4.4 29.4 1.0
N N:GLY45 4.5 34.0 1.0
CA N:SER441 4.6 28.5 1.0
CA N:GLY45 4.6 32.7 1.0
C N:THR46 4.7 37.5 1.0
CD2 N:LEU41 4.7 29.9 1.0
OD2 N:ASP442 4.9 32.9 1.0
CB N:SER441 4.9 31.7 1.0

Reference:

A.Shimada, J.Baba, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara. Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed-Valence State at 1.68 Angstrom Resolution (50 K) To Be Published.
Page generated: Tue Dec 15 10:26:46 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy