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Sodium in PDB 5xdq: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, 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) 134.45 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.307, 205.904, 177.526, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19

Other elements in 5xdq:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 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 Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution (pdb code 5xdq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5xdq

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Sodium binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:30.1
occ:1.00
 OE1 A:GLU40 2.2 30.3 1.0
O A:SER441 2.3 30.3 1.0
O A:GLY45 2.3 34.0 1.0
O A:GLU40 2.3 31.8 1.0
O A:HOH863 2.3 31.4 1.0
CD A:GLU40 3.2 31.4 1.0
C A:GLU40 3.3 30.1 1.0
O A:HOH827 3.4 45.4 1.0
C A:GLY45 3.5 34.8 1.0
C A:SER441 3.5 29.0 1.0
CG A:GLU40 3.5 28.9 1.0
O A:GLN43 4.0 34.4 1.0
CA A:ASP442 4.0 30.8 1.0
CA A:THR46 4.1 34.0 1.0
OD1 A:ASP442 4.1 33.4 1.0
CB A:ASP442 4.1 30.2 1.0
CA A:GLU40 4.1 29.8 1.0
N A:THR46 4.2 34.7 1.0
N A:ASP442 4.2 27.7 1.0
N A:LEU41 4.2 29.9 1.0
CG A:ASP442 4.2 31.6 1.0
N A:LEU47 4.3 34.1 1.0
CA A:LEU41 4.4 29.1 1.0
OE2 A:GLU40 4.4 34.2 1.0
CB A:GLU40 4.4 29.0 1.0
N A:GLY45 4.5 33.7 1.0
CA A:GLY45 4.6 33.9 1.0
CA A:SER441 4.6 30.2 1.0
C A:THR46 4.7 35.4 1.0
CD2 A:LEU41 4.7 31.1 1.0
CB A:SER441 4.9 30.0 1.0
OD2 A:ASP442 5.0 31.9 1.0

Sodium binding site 2 out of 4 in 5xdq

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Sodium binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:53.0
occ:1.00
 OE1 C:GLU236 2.1 61.6 1.0
NE2 C:HIS148 2.1 45.1 1.0
NE2 C:HIS232 2.1 37.1 1.0
O C:HOH516 2.4 95.5 1.0
CD C:GLU236 2.9 51.5 1.0
CD2 C:HIS232 2.9 32.2 1.0
CE1 C:HIS148 3.1 43.4 1.0
CD2 C:HIS148 3.2 39.7 1.0
CE1 C:HIS232 3.2 34.3 1.0
CG C:GLU236 3.4 38.2 1.0
OE2 C:GLU236 3.8 48.0 1.0
SD C:MET152 4.1 40.7 0.8
O C:HOH506 4.1 86.6 1.0
CG C:MET152 4.2 33.2 0.8
CG C:HIS232 4.2 31.1 1.0
ND1 C:HIS148 4.2 44.0 1.0
CG C:MET152 4.3 31.2 0.2
ND1 C:HIS232 4.3 32.0 1.0
CG C:HIS148 4.3 37.8 1.0
SD C:MET152 4.4 33.6 0.2
O C:HOH511 4.7 50.2 1.0
O C:HOH402 4.8 34.8 1.0
CB C:GLU236 4.9 30.2 1.0

Sodium binding site 3 out of 4 in 5xdq

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Sodium binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:41.7
occ:1.00
 OE1 N:GLU40 2.2 44.3 1.0
O N:GLY45 2.2 45.7 1.0
O N:SER441 2.2 42.6 1.0
O N:GLU40 2.3 42.6 1.0
O N:HOH875 2.4 43.7 1.0
CD N:GLU40 3.2 43.6 1.0
C N:GLU40 3.3 40.4 1.0
O N:HOH796 3.4 50.5 1.0
C N:GLY45 3.4 46.9 1.0
C N:SER441 3.5 42.2 1.0
CG N:GLU40 3.5 41.5 1.0
O N:GLN43 4.0 44.9 1.0
CA N:ASP442 4.0 41.4 1.0
CA N:THR46 4.1 48.9 1.0
CA N:GLU40 4.1 39.7 1.0
OD1 N:ASP442 4.1 45.7 1.0
CB N:ASP442 4.2 41.3 1.0
N N:THR46 4.2 48.1 1.0
N N:ASP442 4.2 40.5 1.0
N N:LEU41 4.2 39.3 1.0
CG N:ASP442 4.3 44.6 1.0
N N:LEU47 4.3 47.0 1.0
CB N:GLU40 4.3 40.0 1.0
OE2 N:GLU40 4.4 44.6 1.0
N N:GLY45 4.4 46.8 1.0
CA N:LEU41 4.4 41.4 1.0
CA N:GLY45 4.5 45.5 1.0
CA N:SER441 4.6 41.3 1.0
C N:THR46 4.7 45.4 1.0
CD2 N:LEU41 4.7 39.1 1.0
CB N:SER441 4.9 43.2 1.0
OD2 N:ASP442 5.0 44.6 1.0

Sodium binding site 4 out of 4 in 5xdq

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Sodium binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na302

b:49.7
occ:1.00
 OE1 P:GLU236 2.1 66.3 1.0
NE2 P:HIS148 2.1 47.2 1.0
NE2 P:HIS232 2.1 38.9 1.0
CD P:GLU236 2.9 50.9 1.0
CD2 P:HIS232 3.0 36.5 1.0
CE1 P:HIS148 3.1 43.0 1.0
CD2 P:HIS148 3.2 40.1 1.0
CE1 P:HIS232 3.2 35.9 1.0
CG P:GLU236 3.4 39.2 1.0
OE2 P:GLU236 3.9 47.3 1.0
O P:HOH486 3.9 77.8 1.0
SD P:MET152 4.1 43.0 1.0
CG P:HIS232 4.2 35.0 1.0
CG P:MET152 4.2 34.9 1.0
ND1 P:HIS148 4.2 45.5 1.0
ND1 P:HIS232 4.3 32.5 1.0
CG P:HIS148 4.3 38.2 1.0
O P:HOH488 4.7 56.0 1.0
O P:HOH519 4.7 86.5 1.0
CB P:GLU236 4.8 31.6 1.0
O P:HOH401 4.9 35.8 1.0

Reference:

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase Crystallized at A Neutral pH Using A Fluorinated Detergent. Acta Crystallogr F Struct V. 73 416 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28695851
DOI: 10.1107/S2053230X17008834
Page generated: Tue Oct 8 01:13:40 2024

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