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Sodium in PDB 5iy5: Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

Enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

All present enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5 was solved by S.Shimada, J.Baba, S.Aoe, A.Shimada, E.Yamashita, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.290, 183.872, 148.929, 90.00, 102.12, 90.00
R / Rfree (%) 16.7 / 20.7

Other elements in 5iy5:

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 6 atoms
Copper (Cu) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution (pdb code 5iy5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5iy5

Go back to Sodium Binding Sites List in 5iy5
Sodium binding site 1 out of 4 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:31.8
occ:1.00
OE1 A:GLU40 2.3 31.8 1.0
O A:GLY45 2.3 32.8 1.0
O A:GLU40 2.3 31.4 1.0
O A:SER441 2.3 32.0 1.0
O A:HOH783 2.3 30.4 1.0
CD A:GLU40 3.2 36.8 1.0
C A:GLU40 3.3 31.7 1.0
CG A:GLU40 3.4 33.3 1.0
O A:HOH770 3.4 46.7 1.0
C A:GLY45 3.5 33.9 1.0
C A:SER441 3.5 32.2 1.0
O A:GLN43 4.0 33.1 1.0
CA A:THR46 4.0 38.2 1.0
CA A:ASP442 4.1 30.7 1.0
CA A:GLU40 4.2 31.6 1.0
N A:THR46 4.2 32.8 1.0
CB A:ASP442 4.2 27.5 1.0
N A:LEU47 4.2 37.4 1.0
N A:LEU41 4.2 29.2 1.0
OD1 A:ASP442 4.3 28.3 1.0
N A:ASP442 4.3 31.8 1.0
CG A:ASP442 4.3 28.8 1.0
CB A:GLU40 4.4 32.1 1.0
CA A:LEU41 4.4 29.1 1.0
OE2 A:GLU40 4.4 36.1 1.0
N A:GLY45 4.4 31.5 1.0
C A:THR46 4.6 38.2 1.0
CA A:GLY45 4.6 31.7 1.0
CA A:SER441 4.6 31.7 1.0
CD2 A:LEU41 4.8 31.2 1.0
CB A:SER441 4.9 29.9 1.0

Sodium binding site 2 out of 4 in 5iy5

Go back to Sodium Binding Sites List in 5iy5
Sodium binding site 2 out of 4 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:59.7
occ:1.00
OE1 C:GLU236 2.2 80.0 1.0
NE2 C:HIS232 2.2 33.8 1.0
NE2 C:HIS148 2.2 50.0 1.0
CD2 C:HIS232 3.1 34.1 1.0
CE1 C:HIS148 3.1 45.9 1.0
CD C:GLU236 3.2 56.8 1.0
CE1 C:HIS232 3.3 33.9 1.0
CD2 C:HIS148 3.3 40.8 1.0
CG C:GLU236 3.8 43.7 1.0
O C:HOH522 3.8 66.1 1.0
SD C:MET152 3.9 40.1 1.0
CG C:MET152 4.0 32.5 1.0
OE2 C:GLU236 4.1 56.6 1.0
ND1 C:HIS148 4.3 45.0 1.0
CG C:HIS232 4.3 35.9 1.0
ND1 C:HIS232 4.4 31.0 1.0
CG C:HIS148 4.5 41.9 1.0
O C:HOH411 4.8 37.0 1.0
O C:HOH450 4.9 59.7 1.0
CE C:MET152 4.9 34.6 1.0
O C:HOH416 4.9 72.4 1.0

Sodium binding site 3 out of 4 in 5iy5

Go back to Sodium Binding Sites List in 5iy5
Sodium binding site 3 out of 4 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na604

b:45.1
occ:1.00
OE1 N:GLU40 2.2 43.1 1.0
O N:GLY45 2.3 52.4 1.0
O N:SER441 2.3 42.9 1.0
O N:GLU40 2.3 45.1 1.0
O N:HOH806 2.3 46.9 1.0
CD N:GLU40 3.2 47.8 1.0
O N:HOH788 3.3 53.2 1.0
C N:GLU40 3.4 41.7 1.0
C N:GLY45 3.5 50.1 1.0
CG N:GLU40 3.5 42.1 1.0
C N:SER441 3.5 45.0 1.0
O N:GLN43 3.9 47.0 1.0
CA N:ASP442 4.0 42.9 1.0
CA N:THR46 4.1 53.5 1.0
OD1 N:ASP442 4.1 44.6 1.0
CB N:ASP442 4.2 46.0 1.0
N N:THR46 4.2 51.6 1.0
CA N:GLU40 4.2 41.8 1.0
CG N:ASP442 4.2 52.1 1.0
N N:LEU41 4.2 40.3 1.0
N N:ASP442 4.2 44.8 1.0
CA N:LEU41 4.3 42.2 1.0
OE2 N:GLU40 4.4 46.7 1.0
N N:LEU47 4.4 56.8 1.0
CB N:GLU40 4.4 44.6 1.0
CD2 N:LEU41 4.5 39.0 1.0
N N:GLY45 4.6 50.0 1.0
CA N:GLY45 4.6 48.3 1.0
CA N:SER441 4.7 43.5 1.0
C N:THR46 4.8 60.2 1.0
CB N:SER441 4.9 44.1 1.0
OD2 N:ASP442 5.0 51.9 1.0

Sodium binding site 4 out of 4 in 5iy5

Go back to Sodium Binding Sites List in 5iy5
Sodium binding site 4 out of 4 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na302

b:57.5
occ:1.00
O P:HOH492 2.0 83.2 1.0
NE2 P:HIS232 2.2 39.5 1.0
NE2 P:HIS148 2.2 46.1 1.0
OE1 P:GLU236 2.2 76.3 1.0
CD2 P:HIS232 3.0 36.5 1.0
CD P:GLU236 3.1 49.7 1.0
CE1 P:HIS148 3.1 48.7 1.0
CD2 P:HIS148 3.3 41.4 1.0
CE1 P:HIS232 3.3 35.6 1.0
CG P:GLU236 3.6 41.1 1.0
OE2 P:GLU236 3.9 48.9 1.0
SD P:MET152 4.1 44.7 1.0
CG P:MET152 4.1 37.5 1.0
CG P:HIS232 4.3 37.8 1.0
ND1 P:HIS148 4.3 46.6 1.0
ND1 P:HIS232 4.4 36.7 1.0
CG P:HIS148 4.4 41.2 1.0
O P:HOH424 4.8 36.4 1.0
CB P:GLU236 5.0 31.4 1.0

Reference:

S.Shimada, K.Shinzawa-Itoh, J.Baba, S.Aoe, A.Shimada, E.Yamashita, J.Kang, M.Tateno, S.Yoshikawa, T.Tsukihara. Complex Structure of Cytochrome C-Cytochrome C Oxidase Reveals A Novel Protein-Protein Interaction Mode Embo J. V. 36 291 2017.
ISSN: ESSN 1460-2075
PubMed: 27979921
DOI: 10.15252/EMBJ.201695021
Page generated: Tue Dec 15 11:06:56 2020

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