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Sodium in PDB 5xdx: Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx 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) 40.00 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.044, 205.691, 177.797, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.3

Other elements in 5xdx:

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution (pdb code 5xdx). 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5xdx

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Sodium binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:30.7
occ:1.00
 O A:GLY45 2.3 33.1 1.0
OE1 A:GLU40 2.3 32.7 1.0
O A:GLU40 2.3 31.7 1.0
O A:SER441 2.3 31.3 1.0
O A:HOH832 2.3 28.9 1.0
CD A:GLU40 3.2 33.3 1.0
C A:GLU40 3.3 31.4 1.0
C A:GLY45 3.4 35.0 1.0
O A:HOH808 3.5 38.4 1.0
C A:SER441 3.5 31.2 1.0
CG A:GLU40 3.5 31.9 1.0
O A:HOH880 3.7 40.1 1.0
O A:GLN43 4.0 35.0 1.0
CA A:ASP442 4.0 31.1 1.0
CA A:THR46 4.0 38.1 1.0
CB A:ASP442 4.0 32.1 1.0
OD1 A:ASP442 4.1 33.8 1.0
CG A:ASP442 4.1 33.8 1.0
N A:THR46 4.1 37.7 1.0
N A:ASP442 4.2 30.6 1.0
N A:LEU41 4.2 30.5 1.0
CA A:GLU40 4.2 31.4 1.0
CA A:LEU41 4.3 31.1 1.0
OE2 A:GLU40 4.4 34.8 1.0
N A:LEU47 4.4 38.1 1.0
CB A:GLU40 4.4 31.1 1.0
N A:GLY45 4.5 33.8 1.0
CA A:GLY45 4.5 34.8 1.0
C A:THR46 4.6 39.8 1.0
CA A:SER441 4.7 32.3 1.0
CD2 A:LEU41 4.7 29.0 1.0
OD2 A:ASP442 4.8 34.1 1.0
CB A:SER441 5.0 32.2 1.0

Sodium binding site 2 out of 4 in 5xdx

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Sodium binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:51.3
occ:1.00
 NE2 C:HIS148 2.1 46.8 1.0
NE2 C:HIS232 2.1 42.8 1.0
OE1 C:GLU236 2.1 58.8 1.0
O C:HOH448 2.2 74.1 1.0
CD C:GLU236 2.9 51.0 1.0
CD2 C:HIS232 2.9 39.9 1.0
CE1 C:HIS148 3.0 44.7 1.0
CD2 C:HIS148 3.2 43.6 1.0
CE1 C:HIS232 3.2 41.7 1.0
CG C:GLU236 3.4 45.3 1.0
OE2 C:GLU236 3.8 50.2 1.0
CE C:MET152 4.1 40.1 0.2
SD C:MET152 4.1 39.0 0.8
CG C:MET152 4.1 37.7 0.8
CG C:HIS232 4.2 39.9 1.0
ND1 C:HIS148 4.2 43.9 1.0
ND1 C:HIS232 4.3 40.7 1.0
CG C:HIS148 4.3 42.1 1.0
O C:HOH474 4.8 49.7 1.0
O C:HOH402 4.8 35.7 1.0
CB C:GLU236 4.9 39.1 1.0

Sodium binding site 3 out of 4 in 5xdx

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Sodium binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:49.2
occ:1.00
 OE1 N:GLU40 2.2 50.2 1.0
O N:HOH850 2.2 40.8 1.0
O N:GLY45 2.2 53.9 1.0
O N:GLU40 2.3 48.1 1.0
O N:SER441 2.3 49.9 1.0
CD N:GLU40 3.2 49.9 1.0
C N:GLU40 3.3 47.7 1.0
C N:GLY45 3.4 56.1 1.0
O N:HOH805 3.4 55.5 1.0
C N:SER441 3.5 49.3 1.0
CG N:GLU40 3.5 48.2 1.0
O N:HOH724 3.8 57.1 1.0
CA N:ASP442 3.9 49.4 1.0
CA N:THR46 4.0 58.7 1.0
O N:GLN43 4.0 53.0 1.0
CB N:ASP442 4.0 50.0 1.0
OD1 N:ASP442 4.1 50.9 1.0
CG N:ASP442 4.1 51.7 1.0
N N:ASP442 4.1 49.3 1.0
N N:THR46 4.1 57.5 1.0
CA N:GLU40 4.2 48.1 1.0
N N:LEU41 4.2 46.8 1.0
CA N:LEU41 4.3 46.8 1.0
OE2 N:GLU40 4.4 51.3 1.0
CB N:GLU40 4.4 47.8 1.0
N N:GLY45 4.4 55.5 1.0
N N:LEU47 4.5 59.0 1.0
CA N:GLY45 4.6 55.8 1.0
C N:THR46 4.6 59.8 1.0
CA N:SER441 4.6 49.0 1.0
OD2 N:ASP442 4.8 52.7 1.0
CD2 N:LEU41 4.8 45.7 1.0
CB N:SER441 5.0 50.0 1.0

Sodium binding site 4 out of 4 in 5xdx

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Sodium binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na302

b:51.8
occ:1.00
 O P:HOH458 2.0 70.0 1.0
NE2 P:HIS232 2.1 43.5 1.0
OE1 P:GLU236 2.1 61.0 1.0
NE2 P:HIS148 2.1 48.1 1.0
CD2 P:HIS232 2.9 40.5 1.0
CD P:GLU236 2.9 54.4 1.0
CE1 P:HIS148 3.1 46.6 1.0
CD2 P:HIS148 3.2 45.1 1.0
CE1 P:HIS232 3.3 41.5 1.0
CG P:GLU236 3.3 47.6 1.0
OE2 P:GLU236 3.8 52.1 1.0
SD P:MET152 3.9 41.9 0.7
CG P:MET152 4.1 39.4 0.7
CG P:HIS232 4.1 41.2 1.0
ND1 P:HIS148 4.2 47.7 1.0
ND1 P:HIS232 4.3 40.3 1.0
CG P:HIS148 4.3 43.6 1.0
CG P:MET152 4.5 37.8 0.3
O P:HOH420 4.7 63.1 1.0
O P:HOH403 4.8 40.4 1.0
SD P:MET152 4.8 38.1 0.3
CB P:GLU236 4.8 40.6 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 in the Ligand-Free Reduced State at Neutral pH. Acta Crystallogr F Struct V. 74 92 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29400318
DOI: 10.1107/S2053230X17018532
Page generated: Tue Oct 8 01:13:51 2024

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