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Sodium in PDB 7d5x: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x 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) 39.70 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.767, 203.304, 177.566, 90, 90, 90
R / Rfree (%) 15.6 / 18.4

Other elements in 7d5x:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Magnesium (Mg) 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution (pdb code 7d5x). 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, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7d5x

Go back to Sodium Binding Sites List in 7d5x
Sodium binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:27.4
occ:1.00
 O A:HOH872 2.1 26.3 1.0
OE1 A:GLU40 2.3 30.0 1.0
O A:SER441 2.3 27.5 1.0
O A:GLY45 2.3 29.9 1.0
O A:GLU40 2.4 26.8 1.0
CD A:GLU40 3.3 32.6 1.0
C A:GLU40 3.4 28.0 1.0
O A:HOH837 3.4 35.9 1.0
CG A:GLU40 3.4 25.8 1.0
C A:SER441 3.5 30.0 1.0
C A:GLY45 3.5 31.3 1.0
CA A:ASP442 3.9 25.1 1.0
O A:GLN43 3.9 28.7 1.0
CB A:ASP442 4.0 25.1 1.0
CA A:THR46 4.0 30.1 1.0
O A:HOH858 4.0 37.7 1.0
CG A:ASP442 4.1 29.0 1.0
OD1 A:ASP442 4.1 27.8 1.0
N A:ASP442 4.2 24.6 1.0
CA A:GLU40 4.2 23.8 1.0
N A:THR46 4.2 31.7 1.0
N A:LEU41 4.3 25.3 1.0
CA A:LEU41 4.3 23.2 1.0
N A:LEU47 4.4 31.3 1.0
OE2 A:GLU40 4.4 31.9 1.0
CB A:GLU40 4.5 25.2 1.0
N A:GLY45 4.5 28.4 1.0
CD2 A:LEU41 4.6 24.2 1.0
CA A:GLY45 4.6 31.0 1.0
C A:THR46 4.6 30.6 1.0
CA A:SER441 4.7 25.5 1.0
OD2 A:ASP442 4.8 29.1 1.0
CB A:SER441 5.0 29.8 1.0
C A:PRO44 5.0 29.5 1.0

Sodium binding site 2 out of 4 in 7d5x

Go back to Sodium Binding Sites List in 7d5x
Sodium binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:40.0
occ:1.00
 O C:HOH523 2.2 69.3 1.0
NE2 C:HIS148 2.3 35.1 1.0
NE2 C:HIS232 2.4 29.2 1.0
CD2 C:HIS232 3.2 27.8 1.0
CE1 C:HIS148 3.2 50.4 1.0
CD C:GLU236 3.2 66.5 1.0
CD2 C:HIS148 3.3 37.9 1.0
CG C:GLU236 3.4 38.8 1.0
OE1 C:GLU236 3.5 48.1 1.0
CE1 C:HIS232 3.5 33.7 1.0
OE2 C:GLU236 3.7 44.9 1.0
O C:HOH506 4.0 64.2 1.0
SD C:MET152 4.1 38.7 1.0
CG C:MET152 4.1 30.2 1.0
ND1 C:HIS148 4.3 44.3 1.0
CG C:HIS148 4.4 37.4 1.0
CG C:HIS232 4.4 26.7 1.0
ND1 C:HIS232 4.6 26.7 1.0
O C:HOH499 4.8 46.4 1.0
CB C:GLU236 4.9 25.4 1.0
CE C:MET152 5.0 30.6 1.0
O C:HOH415 5.0 29.9 1.0

Sodium binding site 3 out of 4 in 7d5x

Go back to Sodium Binding Sites List in 7d5x
Sodium binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:31.0
occ:1.00
 O N:HOH878 2.1 30.8 1.0
OE1 N:GLU40 2.3 34.1 1.0
O N:GLY45 2.3 33.8 1.0
O N:SER441 2.3 32.8 1.0
O N:GLU40 2.4 34.1 1.0
CD N:GLU40 3.2 37.1 1.0
C N:GLU40 3.4 35.5 1.0
O N:HOH799 3.5 38.0 1.0
CG N:GLU40 3.5 30.5 1.0
C N:SER441 3.5 31.3 1.0
C N:GLY45 3.5 46.5 1.0
CA N:ASP442 3.9 31.8 1.0
CB N:ASP442 3.9 30.8 1.0
O N:GLN43 4.0 32.8 1.0
O N:HOH837 4.1 40.6 1.0
CA N:THR46 4.1 37.1 1.0
CG N:ASP442 4.1 32.0 1.0
OD1 N:ASP442 4.1 32.4 1.0
N N:ASP442 4.2 29.4 1.0
N N:LEU41 4.2 30.8 1.0
CA N:LEU41 4.2 31.6 1.0
CA N:GLU40 4.3 30.9 1.0
N N:THR46 4.3 38.6 1.0
OE2 N:GLU40 4.4 33.7 1.0
N N:GLY45 4.5 33.9 1.0
CD2 N:LEU41 4.5 29.3 1.0
CB N:GLU40 4.5 31.3 1.0
N N:LEU47 4.5 38.2 1.0
CA N:GLY45 4.6 35.5 1.0
CA N:SER441 4.7 29.5 1.0
C N:THR46 4.7 40.9 1.0
OD2 N:ASP442 4.9 33.5 1.0
CB N:SER441 5.0 38.4 1.0

Sodium binding site 4 out of 4 in 7d5x

Go back to Sodium Binding Sites List in 7d5x
Sodium binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na302

b:39.8
occ:1.00
 NE2 P:HIS148 2.3 36.4 1.0
NE2 P:HIS232 2.5 26.3 1.0
CE1 P:HIS148 3.2 50.0 1.0
CD2 P:HIS232 3.3 28.3 1.0
CD2 P:HIS148 3.3 33.6 1.0
CD P:GLU236 3.4 105.2 1.0
CG P:GLU236 3.4 37.6 1.0
CE1 P:HIS232 3.6 26.8 1.0
OE1 P:GLU236 3.6 54.9 1.0
OE2 P:GLU236 3.7 47.8 1.0
SD P:MET152 4.0 39.3 1.0
CG P:MET152 4.1 33.0 1.0
ND1 P:HIS148 4.4 43.7 1.0
CG P:HIS148 4.4 32.4 1.0
CG P:HIS232 4.5 25.7 1.0
ND1 P:HIS232 4.6 25.2 1.0
CB P:GLU236 4.9 26.3 1.0
O P:HOH455 4.9 29.7 1.0
CE P:MET152 5.0 29.0 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 16:32:10 2024

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