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Sodium in PDB 2ein: Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

All present enzymatic activity of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2ein was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.810, 203.581, 177.927, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.8

Other elements in 2ein:

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 14 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 2ein). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2ein:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2ein

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

b:48.8
occ:1.00
OE1 A:GLU40 2.2 56.0 1.0
O A:SER441 2.3 39.8 1.0
O A:GLU40 2.4 47.4 1.0
O A:GLY45 2.4 59.6 1.0
O A:HOH2026 2.6 41.0 1.0
CD A:GLU40 3.1 58.0 1.0
C A:GLU40 3.3 40.8 1.0
CG A:GLU40 3.4 52.5 1.0
C A:SER441 3.5 38.0 1.0
O A:HOH2060 3.6 63.2 1.0
C A:GLY45 3.6 56.4 1.0
CA A:ASP442 3.9 36.7 1.0
O A:GLN43 4.0 47.0 1.0
CB A:ASP442 4.1 34.7 1.0
CA A:THR46 4.1 60.2 1.0
CA A:GLU40 4.1 45.7 1.0
N A:LEU41 4.1 32.7 1.0
N A:ASP442 4.2 38.7 1.0
CA A:LEU41 4.2 33.0 1.0
OD2 A:ASP442 4.2 39.8 1.0
CB A:GLU40 4.3 45.6 1.0
N A:THR46 4.3 55.7 1.0
OE2 A:GLU40 4.3 54.8 1.0
CG A:ASP442 4.4 36.9 1.0
N A:LEU47 4.5 76.6 1.0
N A:GLY45 4.5 44.6 1.0
CD2 A:LEU41 4.5 36.6 1.0
CA A:SER441 4.6 37.2 1.0
C A:THR46 4.7 69.5 1.0
CA A:GLY45 4.7 52.0 1.0
CE2 A:TYR443 4.8 47.4 1.0
OG1 A:THR46 4.9 65.5 1.0
C A:PRO44 4.9 48.0 1.0

Sodium binding site 2 out of 2 in 2ein

Go back to Sodium Binding Sites List in 2ein
Sodium binding site 2 out of 2 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na1519

b:59.2
occ:1.00
OE1 N:GLU40 2.2 76.2 1.0
O N:GLU40 2.3 59.8 1.0
O N:SER441 2.3 52.7 1.0
O N:GLY45 2.4 65.3 1.0
O N:HOH3026 2.5 62.2 1.0
CD N:GLU40 3.1 75.7 1.0
C N:GLU40 3.3 59.6 1.0
CG N:GLU40 3.4 68.3 1.0
O N:HOH3060 3.5 63.3 1.0
C N:SER441 3.5 49.4 1.0
C N:GLY45 3.6 64.4 1.0
CA N:ASP442 4.0 50.9 1.0
O N:GLN43 4.0 55.7 1.0
N N:LEU41 4.1 59.7 1.0
CA N:GLU40 4.1 59.6 1.0
OD2 N:ASP442 4.2 57.0 1.0
CA N:THR46 4.2 73.3 1.0
N N:ASP442 4.2 45.1 1.0
CA N:LEU41 4.2 60.6 1.0
OE2 N:GLU40 4.3 79.1 1.0
CB N:GLU40 4.3 60.8 1.0
CB N:ASP442 4.3 59.1 1.0
N N:THR46 4.4 68.1 1.0
CG N:ASP442 4.4 60.5 1.0
N N:GLY45 4.5 56.4 1.0
N N:LEU47 4.6 84.5 1.0
CD2 N:LEU41 4.6 63.5 1.0
CA N:SER441 4.7 47.0 1.0
CA N:GLY45 4.7 62.4 1.0
C N:THR46 4.8 79.3 1.0
C N:PRO44 4.9 56.6 1.0
CE2 N:TYR443 4.9 51.5 1.0

Reference:

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104
Page generated: Tue Dec 15 05:48:16 2020

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