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Sodium in PDB 2eij: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eij was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.060, 206.584, 178.298, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.4

Other elements in 2eij:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 4 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 the Fully Reduced State (pdb code 2eij). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eij:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2eij

Go back to Sodium Binding Sites List in 2eij
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


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 the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na519

b:25.4
occ:1.00
OE1 A:GLU40 2.2 26.1 1.0
O A:GLU40 2.3 21.2 1.0
O A:SER441 2.3 25.0 1.0
O A:GLY45 2.4 27.6 1.0
O A:HOH2026 2.5 18.2 1.0
CD A:GLU40 3.1 26.5 1.0
C A:GLU40 3.3 18.4 1.0
CG A:GLU40 3.4 24.5 1.0
C A:SER441 3.5 23.2 1.0
C A:GLY45 3.5 25.8 1.0
O A:HOH2060 3.5 31.5 1.0
O A:HOH2069 3.9 25.7 1.0
CA A:THR46 4.0 29.3 1.0
CA A:ASP442 4.0 21.7 1.0
O A:GLN43 4.1 22.3 1.0
CB A:ASP442 4.1 22.1 1.0
CG A:ASP442 4.2 24.5 1.0
CA A:GLU40 4.2 19.6 1.0
N A:THR46 4.2 26.6 1.0
N A:ASP442 4.2 22.2 1.0
OD2 A:ASP442 4.2 22.4 1.0
N A:LEU41 4.2 16.4 1.0
OE2 A:GLU40 4.3 26.9 1.0
CA A:LEU41 4.3 14.6 1.0
CB A:GLU40 4.4 19.5 1.0
N A:LEU47 4.5 33.2 1.0
N A:GLY45 4.6 19.7 1.0
CD2 A:LEU41 4.6 19.3 1.0
C A:THR46 4.6 32.7 1.0
CA A:SER441 4.7 23.1 1.0
CA A:GLY45 4.7 21.9 1.0
OD1 A:ASP442 4.8 26.5 1.0
CB A:SER441 5.0 22.0 1.0

Sodium binding site 2 out of 2 in 2eij

Go back to Sodium Binding Sites List in 2eij
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


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 the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na1519

b:33.1
occ:1.00
OE1 N:GLU40 2.2 31.0 1.0
O N:GLU40 2.3 27.9 1.0
O N:SER441 2.3 31.5 1.0
O N:GLY45 2.4 33.2 1.0
O N:HOH3026 2.5 28.0 1.0
CD N:GLU40 3.1 30.9 1.0
CG N:GLU40 3.3 30.9 1.0
C N:GLU40 3.3 27.8 1.0
O N:HOH3060 3.5 35.6 1.0
C N:GLY45 3.5 31.6 1.0
C N:SER441 3.5 28.7 1.0
CA N:THR46 3.8 35.0 1.0
O N:HOH3069 3.9 37.5 1.0
CA N:ASP442 4.1 27.9 1.0
N N:THR46 4.1 32.3 1.0
CA N:GLU40 4.1 27.5 1.0
OE2 N:GLU40 4.2 33.4 1.0
O N:GLN43 4.2 28.3 1.0
CB N:ASP442 4.2 29.5 1.0
N N:ASP442 4.3 27.9 1.0
N N:LEU41 4.3 27.1 1.0
CB N:GLU40 4.3 29.3 1.0
N N:LEU47 4.3 39.8 1.0
CG N:ASP442 4.4 32.2 1.0
CA N:LEU41 4.4 27.3 1.0
C N:THR46 4.5 39.2 1.0
OD2 N:ASP442 4.5 29.5 1.0
CA N:SER441 4.6 29.0 1.0
CD2 N:LEU41 4.7 28.6 1.0
N N:GLY45 4.7 31.5 1.0
CA N:GLY45 4.7 29.7 1.0
OD1 N:ASP442 4.9 34.0 1.0
CB N:THR46 4.9 37.8 1.0
CB N:SER441 5.0 29.6 1.0

Reference:

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104
Page generated: Tue Dec 15 05:48:09 2020

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