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Sodium in PDB 6juw: Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw was solved by A.Shimada, K.Muramoto, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.88 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.217, 204.650, 177.397, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.8

Other elements in 6juw:

The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 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 Catalitic Intermediates at 1.80 Angstrom Resolution (pdb code 6juw). 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 Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6juw

Go back to Sodium Binding Sites List in 6juw
Sodium binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 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 Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:29.0
occ:1.00
O A:HOH869 2.2 27.6 1.0
OE1 A:GLU40 2.3 34.5 1.0
O A:SER441 2.3 31.6 1.0
O A:GLY45 2.3 35.3 1.0
O A:GLU40 2.4 30.6 1.0
CD A:GLU40 3.2 39.8 1.0
C A:GLU40 3.4 39.1 1.0
O A:HOH825 3.4 40.2 1.0
C A:GLY45 3.5 36.7 1.0
C A:SER441 3.5 32.7 1.0
CG A:GLU40 3.5 26.7 1.0
CA A:ASP442 3.9 29.6 1.0
O A:GLN43 3.9 32.6 1.0
CB A:ASP442 4.0 28.4 1.0
CA A:THR46 4.0 36.2 1.0
CG A:ASP442 4.1 29.8 1.0
OD1 A:ASP442 4.1 33.0 1.0
N A:ASP442 4.2 28.9 1.0
N A:THR46 4.2 34.9 1.0
CA A:GLU40 4.2 27.4 1.0
N A:LEU41 4.3 30.3 1.0
N A:LEU47 4.3 34.9 1.0
CA A:LEU41 4.4 28.8 1.0
OE2 A:GLU40 4.4 32.5 1.0
N A:GLY45 4.5 30.9 1.0
CB A:GLU40 4.5 26.6 1.0
CA A:GLY45 4.6 36.8 1.0
C A:THR46 4.6 39.3 1.0
CA A:SER441 4.7 28.8 1.0
CD2 A:LEU41 4.7 27.1 1.0
OD2 A:ASP442 4.9 32.8 1.0
CB A:SER441 5.0 33.0 1.0

Sodium binding site 2 out of 4 in 6juw

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Sodium binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 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 Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:22.1
occ:1.00
O C:HOH412 1.9 47.1 1.0
OE2 C:GLU236 2.0 0.6 1.0
NE2 C:HIS148 2.0 36.5 1.0
NE2 C:HIS232 2.1 31.7 1.0
CD C:GLU236 2.5 48.2 1.0
CE1 C:HIS148 2.9 52.2 1.0
CD2 C:HIS232 3.0 34.5 1.0
CD2 C:HIS148 3.1 35.2 1.0
OE1 C:GLU236 3.1 72.4 1.0
CE1 C:HIS232 3.2 31.5 1.0
CG C:GLU236 3.4 85.3 1.0
ND1 C:HIS148 4.1 42.5 1.0
CG C:HIS148 4.2 36.5 1.0
CG C:HIS232 4.2 28.5 1.0
CG C:MET152 4.3 40.6 1.0
ND1 C:HIS232 4.3 30.1 1.0
SD C:MET152 4.3 49.4 1.0
CB C:GLU236 4.7 29.9 1.0

Sodium binding site 3 out of 4 in 6juw

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Sodium binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 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 Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:34.1
occ:1.00
O N:HOH844 2.2 33.1 1.0
OE1 N:GLU40 2.3 38.2 1.0
O N:GLY45 2.3 38.4 1.0
O N:SER441 2.3 31.2 1.0
O N:GLU40 2.4 37.3 1.0
CD N:GLU40 3.2 45.1 1.0
C N:GLU40 3.4 35.1 1.0
O N:HOH734 3.4 42.6 1.0
C N:GLY45 3.5 50.1 1.0
CG N:GLU40 3.5 32.7 1.0
C N:SER441 3.5 34.2 1.0
CA N:ASP442 3.9 29.6 1.0
CB N:ASP442 3.9 32.5 1.0
O N:GLN43 4.0 37.0 1.0
OD1 N:ASP442 4.0 38.0 1.0
CG N:ASP442 4.0 37.8 1.0
CA N:THR46 4.1 40.4 1.0
N N:ASP442 4.2 31.4 1.0
N N:LEU41 4.2 31.7 1.0
N N:THR46 4.2 40.2 1.0
CA N:GLU40 4.3 32.0 1.0
CA N:LEU41 4.3 35.1 1.0
OE2 N:GLU40 4.4 36.6 1.0
N N:GLY45 4.4 41.0 1.0
N N:LEU47 4.5 45.1 1.0
CB N:GLU40 4.5 29.1 1.0
CA N:GLY45 4.6 41.1 1.0
CD2 N:LEU41 4.6 31.8 1.0
CA N:SER441 4.6 30.2 1.0
C N:THR46 4.7 56.5 1.0
OD2 N:ASP442 4.7 37.4 1.0
CB N:SER441 4.9 39.7 1.0
C N:PRO44 5.0 36.5 1.0

Sodium binding site 4 out of 4 in 6juw

Go back to Sodium Binding Sites List in 6juw
Sodium binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 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 Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na301

b:22.3
occ:1.00
O P:HOH403 1.7 46.8 1.0
OE2 P:GLU236 2.0 0.8 1.0
NE2 P:HIS148 2.1 34.4 1.0
NE2 P:HIS232 2.2 31.8 1.0
CD P:GLU236 2.8 56.3 1.0
CD2 P:HIS232 2.9 30.2 1.0
CD2 P:HIS148 3.0 32.6 1.0
CE1 P:HIS148 3.1 49.8 1.0
CG P:GLU236 3.2 65.0 1.0
CE1 P:HIS232 3.3 30.5 1.0
OE1 P:GLU236 3.7 73.2 1.0
SD P:MET152 4.2 49.9 1.0
ND1 P:HIS148 4.2 40.8 1.0
CG P:HIS232 4.2 31.0 1.0
CG P:MET152 4.2 38.8 1.0
CG P:HIS148 4.2 32.8 1.0
C1 P:EDO316 4.2 52.2 1.0
ND1 P:HIS232 4.3 31.1 1.0
C2 P:EDO316 4.4 94.7 1.0
CB P:GLU236 4.7 29.8 1.0

Reference:

A.Shimada, Y.Etoh, R.Kitoh-Fujisawa, A.Sasaki, K.Shinzawa-Itoh, T.Hiromoto, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. X-Ray Structures of Catalytic Intermediates of Cytochromecoxidase Provide Insights Into Its O2-Activation and Unidirectional Proton-Pump Mechanisms. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32165497
DOI: 10.1074/JBC.RA119.009596
Page generated: Tue Dec 15 12:25:55 2020

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