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Sodium in PDB 2occ: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 2occ was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.4

Other elements in 2occ:

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

Magnesium (Mg) 2 atoms
Zinc (Zn) 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 at the Fully Oxidized State (pdb code 2occ). 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 at the Fully Oxidized State, PDB code: 2occ:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2occ

Go back to Sodium Binding Sites List in 2occ
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na519

b:26.2
occ:1.00
O A:SER441 2.3 23.6 1.0
O A:GLY45 2.4 28.9 1.0
OE2 A:GLU40 2.4 27.3 1.0
O A:GLU40 2.5 28.9 1.0
CD A:GLU40 3.4 30.0 1.0
C A:GLU40 3.4 24.5 1.0
C A:SER441 3.5 23.4 1.0
C A:GLY45 3.5 26.8 1.0
CG A:GLU40 3.7 27.2 1.0
CA A:ASP442 3.9 21.8 1.0
O A:GLN43 3.9 30.8 1.0
CA A:THR46 4.0 36.9 1.0
CB A:ASP442 4.1 22.4 1.0
N A:ASP442 4.1 24.6 1.0
OD1 A:ASP442 4.1 21.8 1.0
CG A:ASP442 4.2 21.2 1.0
N A:LEU41 4.3 22.2 1.0
N A:THR46 4.3 28.7 1.0
CA A:LEU41 4.3 17.8 1.0
CA A:GLU40 4.3 24.8 1.0
N A:GLY45 4.4 24.9 1.0
OE1 A:GLU40 4.5 29.0 1.0
CD2 A:LEU41 4.6 25.6 1.0
CB A:GLU40 4.6 25.1 1.0
CA A:GLY45 4.6 25.1 1.0
N A:LEU47 4.6 40.4 1.0
CA A:SER441 4.7 24.1 1.0
OD2 A:ASP442 4.8 25.1 1.0
C A:THR46 4.8 40.8 1.0
CB A:THR46 4.9 40.7 1.0
C A:PRO44 5.0 26.1 1.0

Sodium binding site 2 out of 2 in 2occ

Go back to Sodium Binding Sites List in 2occ
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na519

b:43.8
occ:1.00
O N:GLU40 2.4 41.5 1.0
O N:GLY45 2.4 47.2 1.0
O N:SER441 2.4 37.9 1.0
OE2 N:GLU40 2.5 42.0 1.0
C N:GLU40 3.4 40.0 1.0
CD N:GLU40 3.5 43.4 1.0
C N:GLY45 3.5 44.6 1.0
C N:SER441 3.6 34.7 1.0
CG N:GLU40 3.7 39.7 1.0
CA N:ASP442 3.8 31.6 1.0
O N:GLN43 3.9 39.4 1.0
CB N:ASP442 4.1 38.2 1.0
OD1 N:ASP442 4.1 38.1 1.0
CA N:THR46 4.1 49.2 1.0
CG N:ASP442 4.1 40.1 1.0
N N:ASP442 4.2 30.9 1.0
N N:LEU41 4.2 38.6 1.0
CA N:LEU41 4.3 35.2 1.0
N N:THR46 4.3 45.4 1.0
N N:GLY45 4.4 41.3 1.0
CA N:GLU40 4.4 39.8 1.0
CD2 N:LEU41 4.6 34.9 1.0
CA N:GLY45 4.6 42.2 1.0
OE1 N:GLU40 4.6 42.5 1.0
CB N:GLU40 4.6 41.0 1.0
N N:LEU47 4.7 50.6 1.0
CA N:SER441 4.8 35.3 1.0
OD2 N:ASP442 4.8 46.8 1.0
C N:PRO44 4.9 39.6 1.0
C N:THR46 4.9 50.1 1.0
CE2 N:TYR443 4.9 28.3 1.0
CB N:THR46 5.0 50.7 1.0
C N:GLN43 5.0 40.0 1.0

Reference:

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723
Page generated: Tue Dec 15 05:52:21 2020

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