Atomistry » Sodium » PDB 5inb-5j2c » 5iy5
Atomistry »
  Sodium »
    PDB 5inb-5j2c »
      5iy5 »

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: Mon Oct 7 21:45:08 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy