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Sodium in PDB 7cp5: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution, PDB code: 7cp5 was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.91 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.589, 203.218, 177.702, 90, 90, 90
R / Rfree (%) 16 / 18.9

Other elements in 7cp5:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution (pdb code 7cp5). 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution, PDB code: 7cp5:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7cp5

Go back to Sodium Binding Sites List in 7cp5
Sodium binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:24.6
occ:1.00
 O A:HOH841 2.2 23.4 1.0
OE1 A:GLU40 2.3 28.3 1.0
O A:GLY45 2.3 29.4 1.0
O A:SER441 2.3 24.1 1.0
O A:GLU40 2.4 25.5 1.0
CD A:GLU40 3.2 26.1 1.0
O A:HOH805 3.3 14.5 0.1
O A:HOH789 3.4 32.9 1.0
C A:GLU40 3.4 26.7 1.0
C A:GLY45 3.5 29.8 1.0
CG A:GLU40 3.5 22.9 1.0
C A:SER441 3.5 27.9 1.0
O A:GLN43 3.9 25.5 1.0
CA A:ASP442 4.0 23.8 1.0
CB A:ASP442 4.0 23.6 1.0
CA A:THR46 4.1 27.2 1.0
OD1 A:ASP442 4.1 26.8 1.0
CG A:ASP442 4.2 27.2 1.0
N A:ASP442 4.2 22.3 1.0
N A:THR46 4.2 28.5 1.0
CA A:GLU40 4.2 22.8 1.0
N A:LEU41 4.3 23.0 1.0
N A:LEU47 4.3 29.4 1.0
CA A:LEU41 4.4 24.1 1.0
OE2 A:GLU40 4.4 29.1 1.0
N A:GLY45 4.4 26.0 1.0
CB A:GLU40 4.5 23.2 1.0
CA A:GLY45 4.6 28.3 1.0
C A:THR46 4.6 33.5 1.0
CD2 A:LEU41 4.7 23.6 1.0
CA A:SER441 4.7 25.8 1.0
OD2 A:ASP442 4.9 25.6 1.0
CB A:SER441 5.0 28.3 1.0

Sodium binding site 2 out of 4 in 7cp5

Go back to Sodium Binding Sites List in 7cp5
Sodium binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:31.2
occ:1.00
 OE1 C:GLU236 2.1 170.9 1.0
NE2 C:HIS148 2.1 33.5 1.0
NE2 C:HIS232 2.3 25.5 1.0
CD2 C:HIS232 3.0 26.4 1.0
CD C:GLU236 3.0 64.6 1.0
CE1 C:HIS148 3.1 42.9 1.0
CD2 C:HIS148 3.1 36.1 1.0
CG C:GLU236 3.2 46.5 1.0
CE1 C:HIS232 3.4 29.4 1.0
CG C:MET152 4.1 32.8 1.0
SD C:MET152 4.1 38.9 1.0
OE2 C:GLU236 4.2 74.0 1.0
ND1 C:HIS148 4.2 36.8 1.0
CG C:HIS232 4.2 24.2 1.0
CG C:HIS148 4.3 39.1 1.0
ND1 C:HIS232 4.4 26.1 1.0
CB C:GLU236 4.8 24.8 1.0

Sodium binding site 3 out of 4 in 7cp5

Go back to Sodium Binding Sites List in 7cp5
Sodium binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na606

b:28.8
occ:1.00
 O N:HOH873 2.2 27.8 1.0
O N:GLY45 2.3 33.1 1.0
OE1 N:GLU40 2.3 29.8 1.0
O N:SER441 2.3 29.1 1.0
O N:GLU40 2.3 31.8 1.0
CD N:GLU40 3.2 36.2 1.0
C N:GLU40 3.4 30.5 1.0
O N:HOH779 3.4 36.8 1.0
CG N:GLU40 3.4 29.3 1.0
C N:GLY45 3.5 42.6 1.0
C N:SER441 3.5 28.9 1.0
CA N:ASP442 4.0 27.8 1.0
CB N:ASP442 4.0 28.5 1.0
O N:GLN43 4.0 30.9 1.0
CA N:THR46 4.1 32.9 1.0
OD1 N:ASP442 4.1 29.7 1.0
CG N:ASP442 4.2 31.0 1.0
CA N:GLU40 4.2 30.9 1.0
N N:ASP442 4.2 29.4 1.0
N N:LEU41 4.2 29.1 1.0
N N:THR46 4.2 36.2 1.0
CA N:LEU41 4.3 33.2 1.0
CB N:GLU40 4.4 28.8 1.0
OE2 N:GLU40 4.4 30.0 1.0
N N:LEU47 4.4 37.5 1.0
N N:GLY45 4.5 31.2 1.0
CA N:GLY45 4.6 31.7 1.0
CD2 N:LEU41 4.6 22.9 1.0
CA N:SER441 4.6 27.7 1.0
C N:THR46 4.7 38.5 1.0
CB N:SER441 4.9 29.5 1.0
OD2 N:ASP442 4.9 30.5 1.0

Sodium binding site 4 out of 4 in 7cp5

Go back to Sodium Binding Sites List in 7cp5
Sodium binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na302

b:30.1
occ:1.00
 O P:HOH515 2.0 52.6 1.0
NE2 P:HIS148 2.2 36.7 1.0
NE2 P:HIS232 2.3 27.6 1.0
CD2 P:HIS232 3.0 28.2 1.0
CD2 P:HIS148 3.1 31.4 1.0
CD P:GLU236 3.2 126.5 1.0
CE1 P:HIS148 3.2 48.7 1.0
CG P:GLU236 3.2 41.9 1.0
CE1 P:HIS232 3.5 28.0 1.0
OE1 P:GLU236 3.5 84.0 1.0
OE2 P:GLU236 3.6 54.9 1.0
CG P:MET152 4.2 33.3 1.0
SD P:MET152 4.2 39.8 1.0
CG P:HIS232 4.3 28.2 1.0
ND1 P:HIS148 4.3 43.9 1.0
CG P:HIS148 4.3 30.1 1.0
ND1 P:HIS232 4.5 25.8 1.0
CB P:GLU236 4.8 25.9 1.0

Reference:

A.Shimada, F.Hara, K.Shinzawa-Itoh, N.Kanehisa, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. Critical Roles of the Cub Site in Efficient Proton Pumping As Revealed By Crystal Structures of Mammalian Cytochrome C Oxidase Catalytic Intermediates J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Tue Oct 8 16:24:33 2024

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