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Sodium in PDB 1v54: 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: 1v54 was solved by T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.7

Other elements in 1v54:

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 1v54). 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: 1v54:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1v54

Go back to Sodium Binding Sites List in 1v54
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:Na3519

b:27.3
occ:1.00
O A:HOH3544 2.0 22.0 1.0
O A:GLY45 2.4 28.3 1.0
O A:SER441 2.4 25.4 1.0
O A:GLU40 2.4 25.0 1.0
OE1 A:GLU40 2.5 25.5 1.0
CD A:GLU40 3.4 27.9 1.0
C A:GLU40 3.4 22.9 1.0
O A:HOH3564 3.5 38.2 1.0
C A:GLY45 3.5 25.5 1.0
C A:SER441 3.6 24.5 1.0
CG A:GLU40 3.7 26.9 1.0
O A:GLN43 3.8 22.4 1.0
CA A:ASP442 3.9 22.0 1.0
OD2 A:ASP442 3.9 24.7 1.0
CB A:ASP442 4.0 23.6 1.0
CG A:ASP442 4.1 25.5 1.0
N A:ASP442 4.2 21.6 1.0
CA A:LEU41 4.2 20.0 1.0
N A:LEU41 4.2 20.7 1.0
CA A:THR46 4.3 26.7 1.0
N A:GLY45 4.3 21.8 1.0
N A:THR46 4.3 25.4 1.0
CA A:GLU40 4.3 24.0 1.0
CD2 A:LEU41 4.5 22.2 1.0
CA A:GLY45 4.5 23.1 1.0
OE2 A:GLU40 4.6 27.5 1.0
CB A:GLU40 4.6 25.3 1.0
N A:LEU47 4.7 30.6 1.0
CA A:SER441 4.7 23.6 1.0
OD1 A:ASP442 4.8 27.9 1.0
C A:PRO44 4.9 24.3 1.0
C A:THR46 4.9 30.6 1.0

Sodium binding site 2 out of 2 in 1v54

Go back to Sodium Binding Sites List in 1v54
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:Na4519

b:31.2
occ:1.00
O N:HOH1026 2.0 29.3 1.0
O N:GLY45 2.3 32.6 1.0
O N:SER441 2.4 27.6 1.0
O N:GLU40 2.4 28.9 1.0
OE1 N:GLU40 2.5 29.9 1.0
C N:GLU40 3.4 26.5 1.0
O N:HOH1060 3.4 42.0 1.0
CD N:GLU40 3.4 29.2 1.0
C N:GLY45 3.5 29.6 1.0
C N:SER441 3.5 26.9 1.0
CG N:GLU40 3.7 29.8 1.0
O N:GLN43 3.9 29.0 1.0
CA N:ASP442 3.9 25.2 1.0
OD2 N:ASP442 4.1 32.1 1.0
CB N:ASP442 4.1 29.2 1.0
CG N:ASP442 4.2 32.5 1.0
CA N:THR46 4.2 30.7 1.0
N N:ASP442 4.2 26.2 1.0
N N:LEU41 4.2 24.8 1.0
CA N:LEU41 4.3 24.4 1.0
N N:THR46 4.3 30.2 1.0
CA N:GLU40 4.3 26.6 1.0
N N:GLY45 4.4 28.2 1.0
CB N:GLU40 4.6 26.6 1.0
CA N:GLY45 4.6 28.7 1.0
OE2 N:GLU40 4.6 30.3 1.0
N N:LEU47 4.6 34.9 1.0
CD2 N:LEU41 4.6 23.1 1.0
CA N:SER441 4.7 28.1 1.0
C N:THR46 4.8 33.2 1.0
OD1 N:ASP442 4.9 35.3 1.0
C N:PRO44 4.9 29.4 1.0

Reference:

T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa. The Low-Spin Heme of Cytochrome C Oxidase As the Driving Element of the Proton-Pumping Process. Proc.Natl.Acad.Sci.Usa V. 100 15304 2003.
ISSN: ISSN 0027-8424
PubMed: 14673090
DOI: 10.1073/PNAS.2635097100
Page generated: Tue Dec 15 05:37:22 2020

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