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Sodium in PDB 7d5w: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution, PDB code: 7d5w 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) 39.92 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.435, 203.092, 177.794, 90, 90, 90
R / Rfree (%) 15.4 / 18.4

Other elements in 7d5w:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution (pdb code 7d5w). 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 O at 1.84 Angstrom Resolution, PDB code: 7d5w:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7d5w

Go back to Sodium Binding Sites List in 7d5w
Sodium binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:24.9
occ:1.00
 O A:HOH867 2.2 23.4 1.0
OE1 A:GLU40 2.3 29.6 1.0
O A:GLY45 2.3 30.6 1.0
O A:SER441 2.3 26.0 1.0
O A:GLU40 2.4 26.1 1.0
CD A:GLU40 3.2 29.0 1.0
C A:GLU40 3.4 24.8 1.0
CG A:GLU40 3.4 25.1 1.0
O A:HOH828 3.4 39.7 1.0
C A:GLY45 3.5 33.9 1.0
O A:HOH729 3.5 27.7 0.2
C A:SER441 3.6 28.7 1.0
CB A:ASP442 3.9 23.5 1.0
CA A:ASP442 4.0 23.3 1.0
O A:GLN43 4.0 27.1 1.0
CA A:THR46 4.1 31.2 1.0
OD1 A:ASP442 4.1 29.5 1.0
CG A:ASP442 4.1 25.0 1.0
N A:THR46 4.2 31.6 1.0
N A:ASP442 4.2 21.8 1.0
CA A:GLU40 4.2 22.8 1.0
N A:LEU41 4.3 24.5 1.0
CA A:LEU41 4.3 25.1 1.0
N A:LEU47 4.4 30.3 1.0
OE2 A:GLU40 4.4 29.2 1.0
N A:GLY45 4.4 27.4 1.0
CB A:GLU40 4.5 22.4 1.0
CA A:GLY45 4.6 29.4 1.0
CD2 A:LEU41 4.6 22.3 1.0
CA A:SER441 4.7 27.0 1.0
C A:THR46 4.7 38.4 1.0
OD2 A:ASP442 4.9 26.4 1.0
CB A:SER441 5.0 27.0 1.0

Sodium binding site 2 out of 4 in 7d5w

Go back to Sodium Binding Sites List in 7d5w
Sodium binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:36.8
occ:1.00
 O C:HOH524 2.2 69.6 1.0
NE2 C:HIS148 2.2 36.4 1.0
NE2 C:HIS232 2.4 28.9 1.0
CD2 C:HIS232 3.1 27.4 1.0
CD2 C:HIS148 3.2 35.1 1.0
CE1 C:HIS148 3.2 44.3 1.0
CD C:GLU236 3.3 53.9 1.0
CG C:GLU236 3.4 39.2 1.0
CE1 C:HIS232 3.5 35.0 1.0
OE2 C:GLU236 3.6 47.7 1.0
OE1 C:GLU236 3.7 51.1 1.0
CG C:MET152 4.0 28.8 1.0
SD C:MET152 4.1 39.6 1.0
ND1 C:HIS148 4.3 41.6 1.0
CG C:HIS148 4.4 37.5 1.0
CG C:HIS232 4.4 25.8 1.0
ND1 C:HIS232 4.5 25.1 1.0
O C:HOH495 4.8 48.9 1.0
CB C:GLU236 4.9 23.4 1.0
O C:HOH421 5.0 27.4 1.0

Sodium binding site 3 out of 4 in 7d5w

Go back to Sodium Binding Sites List in 7d5w
Sodium binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na606

b:30.2
occ:1.00
 O N:HOH881 2.2 28.6 1.0
O N:GLY45 2.3 33.1 1.0
OE1 N:GLU40 2.3 31.6 1.0
O N:SER441 2.3 31.1 1.0
O N:GLU40 2.3 30.4 1.0
CD N:GLU40 3.2 46.6 1.0
C N:GLU40 3.3 33.2 1.0
CG N:GLU40 3.5 31.7 1.0
C N:GLY45 3.5 48.4 1.0
O N:HOH846 3.5 37.2 1.0
C N:SER441 3.5 29.2 1.0
CA N:ASP442 4.0 33.2 1.0
O N:GLN43 4.0 33.9 1.0
CB N:ASP442 4.0 31.7 1.0
OD1 N:ASP442 4.1 32.0 1.0
CA N:THR46 4.1 39.9 1.0
CG N:ASP442 4.1 32.0 1.0
CA N:GLU40 4.2 30.3 1.0
N N:LEU41 4.2 31.9 1.0
N N:ASP442 4.2 31.3 1.0
N N:THR46 4.2 37.6 1.0
CA N:LEU41 4.3 32.4 1.0
CB N:GLU40 4.4 29.4 1.0
OE2 N:GLU40 4.4 31.6 1.0
N N:GLY45 4.4 34.9 1.0
N N:LEU47 4.5 41.3 1.0
CA N:GLY45 4.6 31.7 1.0
CD2 N:LEU41 4.6 25.5 1.0
CA N:SER441 4.6 28.4 1.0
C N:THR46 4.8 49.6 1.0
OD2 N:ASP442 4.9 34.1 1.0
CB N:SER441 4.9 31.6 1.0

Sodium binding site 4 out of 4 in 7d5w

Go back to Sodium Binding Sites List in 7d5w
Sodium binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na302

b:38.1
occ:1.00
 O P:HOH530 2.0 58.5 1.0
NE2 P:HIS148 2.2 37.8 1.0
NE2 P:HIS232 2.4 27.3 1.0
CD2 P:HIS232 3.1 26.8 1.0
CD P:GLU236 3.2 80.0 1.0
CD2 P:HIS148 3.2 32.8 1.0
CE1 P:HIS148 3.2 40.8 1.0
CG P:GLU236 3.3 37.6 1.0
OE2 P:GLU236 3.5 52.5 1.0
CE1 P:HIS232 3.6 28.4 1.0
OE1 P:GLU236 3.6 62.3 1.0
SD P:MET152 4.1 38.6 1.0
CG P:MET152 4.2 30.5 1.0
ND1 P:HIS148 4.3 44.4 1.0
CG P:HIS148 4.4 28.9 1.0
CG P:HIS232 4.4 25.9 1.0
ND1 P:HIS232 4.6 25.8 1.0
O P:HOH465 4.6 49.4 1.0
CB P:GLU236 4.8 22.8 1.0
O P:HOH475 4.9 28.1 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 16:30:20 2024

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