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Sodium in PDB 3x2q: X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution

Enzymatic activity of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution

All present enzymatic activity of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution, PDB code: 3x2q was solved by N.Yano, K.Muramoto, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.678, 206.675, 178.201, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.4

Other elements in 3x2q:

The structure of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution 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 X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution (pdb code 3x2q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution, PDB code: 3x2q:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3x2q

Go back to Sodium Binding Sites List in 3x2q
Sodium binding site 1 out of 2 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:45.6
occ:1.00
O A:HOH709 1.4 47.4 1.0
OE1 A:GLU40 2.3 48.9 1.0
O A:GLY45 2.3 46.4 1.0
O A:GLU40 2.4 33.6 1.0
O A:SER441 2.4 34.5 1.0
O A:GLN43 3.1 36.7 1.0
CD A:GLU40 3.3 40.9 1.0
C A:GLU40 3.4 29.4 1.0
C A:GLY45 3.6 44.5 1.0
CG A:GLU40 3.7 34.6 1.0
C A:SER441 3.7 27.1 1.0
OD2 A:ASP442 3.8 31.6 1.0
CA A:ASP442 4.1 28.9 1.0
N A:GLY45 4.1 36.5 1.0
CG A:ASP442 4.2 32.3 1.0
CB A:ASP442 4.3 28.8 1.0
C A:GLN43 4.3 33.4 1.0
N A:LEU41 4.3 28.9 1.0
CA A:GLU40 4.3 29.2 1.0
CA A:LEU41 4.3 28.2 1.0
CA A:THR46 4.3 50.7 1.0
O A:HOH869 4.4 54.4 1.0
N A:THR46 4.4 48.4 1.0
N A:ASP442 4.4 28.4 1.0
OE2 A:GLU40 4.4 35.4 1.0
N A:LEU47 4.5 50.9 1.0
C A:PRO44 4.5 35.7 1.0
CA A:GLY45 4.6 41.0 1.0
CB A:GLU40 4.6 30.4 1.0
CA A:PRO44 4.7 34.4 1.0
CD2 A:LEU41 4.8 27.2 1.0
C A:THR46 4.9 52.2 1.0
OD1 A:ASP442 4.9 31.2 1.0
CE2 A:TYR443 4.9 27.1 1.0
N A:PRO44 4.9 34.3 1.0
C A:LEU41 5.0 28.1 1.0

Sodium binding site 2 out of 2 in 3x2q

Go back to Sodium Binding Sites List in 3x2q
Sodium binding site 2 out of 2 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na606

b:53.7
occ:1.00
O N:HOH701 2.1 52.0 1.0
O N:GLY45 2.3 58.0 1.0
OE1 N:GLU40 2.3 63.8 1.0
O N:GLU40 2.3 47.0 1.0
O N:SER441 2.4 46.5 1.0
O N:GLN43 3.3 49.8 1.0
CD N:GLU40 3.3 54.7 1.0
C N:GLU40 3.4 42.6 1.0
C N:GLY45 3.5 58.5 1.0
C N:SER441 3.6 42.8 1.0
CG N:GLU40 3.7 43.1 1.0
OD2 N:ASP442 3.9 44.9 1.0
CA N:ASP442 4.1 41.0 1.0
N N:GLY45 4.1 53.9 1.0
CG N:ASP442 4.1 43.8 1.0
N N:LEU41 4.2 41.5 1.0
CA N:LEU41 4.3 40.4 1.0
N N:ASP442 4.3 41.8 1.0
CB N:ASP442 4.3 41.0 1.0
CA N:GLU40 4.3 42.5 1.0
CA N:THR46 4.4 63.1 1.0
N N:THR46 4.4 61.0 1.0
C N:GLN43 4.4 49.2 1.0
OE2 N:GLU40 4.4 53.4 1.0
CA N:GLY45 4.5 56.7 1.0
C N:PRO44 4.5 53.2 1.0
CB N:GLU40 4.6 42.4 1.0
CD2 N:LEU41 4.6 33.6 1.0
N N:LEU47 4.7 64.0 1.0
CA N:PRO44 4.7 51.7 1.0
CE2 N:TYR443 4.8 36.6 1.0
OD1 N:ASP442 4.9 47.7 1.0
C N:LEU41 4.9 41.6 1.0
CA N:SER441 4.9 42.7 1.0
C N:THR46 5.0 64.6 1.0

Reference:

N.Yano, K.Muramoto, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara. X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution. Acta Crystallogr F Struct V. 71 726 2015BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 26057802
DOI: 10.1107/S2053230X15007025
Page generated: Tue Dec 15 06:30:37 2020

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