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Sodium in PDB 2eil: Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

All present enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.379, 205.898, 178.182, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.1

Other elements in 2eil:

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Cadmium (Cd) 3 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 2eil). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2eil

Go back to Sodium Binding Sites List in 2eil
Sodium binding site 1 out of 2 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na519

b:41.2
occ:1.00
OE1 A:GLU40 2.2 42.9 1.0
O A:GLU40 2.3 30.8 1.0
O A:SER441 2.4 28.2 1.0
O A:GLY45 2.4 45.6 1.0
O A:HOH2026 2.5 47.4 1.0
O A:HOH2060 2.8 37.7 1.0
CD A:GLU40 3.2 38.3 1.0
C A:GLU40 3.4 25.2 1.0
CG A:GLU40 3.5 33.2 1.0
C A:SER441 3.6 26.1 1.0
C A:GLY45 3.6 42.2 1.0
O A:GLN43 3.7 31.5 1.0
CA A:ASP442 4.1 25.1 1.0
CA A:GLU40 4.2 26.9 1.0
CA A:THR46 4.2 49.3 1.0
N A:LEU41 4.2 23.6 1.0
CB A:ASP442 4.3 28.2 1.0
OE2 A:GLU40 4.3 38.9 1.0
OD2 A:ASP442 4.3 32.8 1.0
N A:ASP442 4.3 25.8 1.0
CG A:ASP442 4.3 31.7 1.0
CA A:LEU41 4.3 20.9 1.0
N A:THR46 4.4 45.2 1.0
N A:LEU47 4.4 56.9 1.0
N A:GLY45 4.4 26.6 1.0
CB A:GLU40 4.4 27.3 1.0
CD2 A:LEU41 4.6 21.7 1.0
CA A:GLY45 4.7 34.0 1.0
CA A:SER441 4.7 24.4 1.0
C A:THR46 4.8 56.0 1.0
C A:PRO44 4.9 29.0 1.0
C A:GLN43 4.9 34.1 1.0
OD1 A:ASP442 4.9 33.8 1.0

Sodium binding site 2 out of 2 in 2eil

Go back to Sodium Binding Sites List in 2eil
Sodium binding site 2 out of 2 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na1519

b:47.4
occ:1.00
OE1 N:GLU40 2.2 47.8 1.0
O N:GLU40 2.3 38.9 1.0
O N:SER441 2.4 36.8 1.0
O N:GLY45 2.4 51.0 1.0
O N:HOH3026 2.6 54.0 1.0
O N:HOH3060 2.9 47.6 1.0
CD N:GLU40 3.0 43.5 1.0
CG N:GLU40 3.3 42.0 1.0
C N:GLU40 3.3 35.4 1.0
C N:SER441 3.6 35.1 1.0
C N:GLY45 3.6 48.5 1.0
O N:GLN43 3.9 36.2 1.0
CA N:THR46 4.0 56.0 1.0
CA N:GLU40 4.1 35.8 1.0
OE2 N:GLU40 4.2 43.1 1.0
CA N:ASP442 4.2 32.2 1.0
N N:LEU47 4.2 62.4 1.0
N N:LEU41 4.3 34.9 1.0
N N:THR46 4.3 51.6 1.0
CB N:GLU40 4.3 37.2 1.0
N N:ASP442 4.3 33.5 1.0
CB N:ASP442 4.4 35.9 1.0
OD2 N:ASP442 4.4 39.5 1.0
CG N:ASP442 4.4 40.2 1.0
CA N:LEU41 4.5 32.2 1.0
N N:GLY45 4.5 43.0 1.0
C N:THR46 4.6 60.5 1.0
CA N:SER441 4.7 36.3 1.0
CA N:GLY45 4.7 44.1 1.0
CD2 N:LEU41 4.8 27.2 1.0
C N:PRO44 5.0 42.0 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 05:48:12 2020

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