Atomistry » Sodium » PDB 7cfs-7d5w » 7d5w
Atomistry »
  Sodium »
    PDB 7cfs-7d5w »
      7d5w »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy