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Sodium in PDB 3abm: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset), PDB code: 3abm was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Other elements in 3abm:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset) 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 (200-S X-Ray Exposure Dataset) (pdb code 3abm). 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 (200-S X-Ray Exposure Dataset), PDB code: 3abm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3abm

Go back to Sodium Binding Sites List in 3abm
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na519

b:42.8
occ:1.00
O A:HOH2026 1.7 46.0 1.0
O A:HOH2060 2.1 22.9 1.0
OE1 A:GLU40 2.3 42.4 1.0
O A:GLU40 2.3 34.7 1.0
O A:GLY45 2.3 42.2 1.0
O A:SER441 2.4 34.4 1.0
CD A:GLU40 3.2 38.1 1.0
O A:GLN43 3.2 33.5 1.0
C A:GLU40 3.5 29.8 1.0
CG A:GLU40 3.5 29.9 1.0
C A:GLY45 3.6 39.3 1.0
C A:SER441 3.7 29.6 1.0
OD2 A:ASP442 3.8 29.2 1.0
CA A:ASP442 4.0 30.2 1.0
CG A:ASP442 4.1 36.2 1.0
CB A:ASP442 4.2 31.2 1.0
N A:GLY45 4.3 30.9 1.0
CA A:GLU40 4.3 29.8 1.0
CA A:THR46 4.3 44.7 1.0
N A:LEU41 4.3 29.5 1.0
OE2 A:GLU40 4.3 35.4 1.0
N A:ASP442 4.4 29.5 1.0
N A:THR46 4.4 41.3 1.0
CA A:LEU41 4.4 27.6 1.0
C A:GLN43 4.5 30.9 1.0
CB A:GLU40 4.5 28.5 1.0
N A:LEU47 4.5 47.4 1.0
O A:HOH2368 4.6 48.6 1.0
CA A:GLY45 4.6 36.8 1.0
CD2 A:LEU41 4.7 29.0 1.0
C A:PRO44 4.7 34.0 1.0
CA A:PRO44 4.8 30.7 1.0
OD1 A:ASP442 4.8 32.9 1.0
C A:THR46 4.9 47.2 1.0
CA A:SER441 4.9 28.6 1.0

Sodium binding site 2 out of 2 in 3abm

Go back to Sodium Binding Sites List in 3abm
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na1519

b:45.9
occ:1.00
O N:HOH3026 2.0 51.0 1.0
O N:HOH3060 2.2 35.1 1.0
OE1 N:GLU40 2.3 48.5 1.0
O N:GLY45 2.3 47.5 1.0
O N:GLU40 2.3 39.6 1.0
O N:SER441 2.3 39.2 1.0
CD N:GLU40 3.1 43.8 1.0
C N:GLU40 3.4 37.4 1.0
O N:GLN43 3.5 41.5 1.0
CG N:GLU40 3.5 39.3 1.0
C N:GLY45 3.5 46.4 1.0
C N:SER441 3.6 36.9 1.0
OD2 N:ASP442 3.9 36.6 1.0
CA N:ASP442 4.0 34.8 1.0
CG N:ASP442 4.1 35.8 1.0
N N:LEU41 4.2 36.4 1.0
OE2 N:GLU40 4.2 43.4 1.0
CB N:ASP442 4.2 34.2 1.0
N N:GLY45 4.2 44.0 1.0
CA N:LEU41 4.3 35.0 1.0
N N:ASP442 4.3 36.9 1.0
CA N:THR46 4.3 48.7 1.0
CA N:GLU40 4.3 36.7 1.0
N N:THR46 4.4 47.3 1.0
CB N:GLU40 4.5 35.4 1.0
CD2 N:LEU41 4.5 31.4 1.0
CA N:GLY45 4.5 44.8 1.0
N N:LEU47 4.5 48.9 1.0
C N:GLN43 4.6 40.9 1.0
C N:PRO44 4.8 43.9 1.0
CA N:SER441 4.8 37.1 1.0
OD1 N:ASP442 4.9 40.4 1.0
C N:THR46 4.9 49.6 1.0
CE2 N:TYR443 5.0 32.2 1.0

Reference:

H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa. A Peroxide Bridge Between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump Proc.Natl.Acad.Sci.Usa V. 106 2165 2009.
ISSN: ISSN 0027-8424
PubMed: 19164527
DOI: 10.1073/PNAS.0806391106
Page generated: Tue Dec 15 06:01:56 2020

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