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

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

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

Protein crystallography data

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eim 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 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.909, 206.721, 178.337, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.6

Other elements in 2eim:

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

Magnesium (Mg) 2 atoms
Zinc (Zn) 6 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 Reduced State (pdb code 2eim). 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 Reduced State, PDB code: 2eim:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2eim

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

b:30.0
occ:1.00
OE1 A:GLU40 2.2 41.9 1.0
O A:SER441 2.3 24.1 1.0
O A:GLU40 2.3 31.3 1.0
O A:GLY45 2.4 41.9 1.0
O A:HOH2026 2.5 22.7 1.0
CD A:GLU40 3.2 43.9 1.0
C A:GLU40 3.3 28.4 1.0
C A:SER441 3.5 26.6 1.0
CG A:GLU40 3.5 39.2 1.0
C A:GLY45 3.6 40.3 1.0
O A:HOH2060 3.7 34.0 1.0
O A:GLN43 3.9 39.5 1.0
O A:HOH2069 3.9 43.6 1.0
CG A:ASP442 4.0 34.5 1.0
CA A:THR46 4.0 44.3 1.0
CA A:ASP442 4.1 26.1 1.0
CB A:ASP442 4.1 28.7 1.0
OD2 A:ASP442 4.2 39.1 1.0
N A:LEU41 4.2 22.1 1.0
CA A:GLU40 4.2 26.0 1.0
N A:ASP442 4.2 27.3 1.0
CA A:LEU41 4.3 18.3 1.0
N A:THR46 4.3 42.8 1.0
CD2 A:LEU41 4.3 25.8 1.0
OE2 A:GLU40 4.3 38.1 1.0
CB A:GLU40 4.4 25.7 1.0
OD1 A:ASP442 4.4 38.1 1.0
N A:GLY45 4.5 38.3 1.0
CA A:SER441 4.6 25.9 1.0
N A:LEU47 4.6 51.0 1.0
CA A:GLY45 4.7 38.7 1.0
C A:THR46 4.7 50.3 1.0
CB A:SER441 5.0 31.9 1.0

Sodium binding site 2 out of 2 in 2eim

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

b:46.3
occ:1.00
OE1 N:GLU40 2.2 43.6 1.0
O N:GLU40 2.3 39.9 1.0
O N:SER441 2.3 39.4 1.0
O N:GLY45 2.4 50.1 1.0
O N:HOH3026 2.6 44.8 1.0
CD N:GLU40 3.1 43.1 1.0
CG N:GLU40 3.2 41.9 1.0
C N:GLU40 3.2 40.9 1.0
C N:SER441 3.5 39.7 1.0
C N:GLY45 3.6 45.0 1.0
O N:HOH3060 3.7 50.6 1.0
CA N:THR46 3.8 53.7 1.0
O N:HOH3069 3.9 39.5 1.0
O N:GLN43 4.0 46.0 1.0
CA N:GLU40 4.1 38.2 1.0
CG N:ASP442 4.1 42.1 1.0
N N:LEU41 4.1 41.2 1.0
CA N:ASP442 4.2 34.1 1.0
N N:THR46 4.2 46.7 1.0
CB N:GLU40 4.2 35.8 1.0
OE2 N:GLU40 4.3 33.9 1.0
CB N:ASP442 4.3 39.2 1.0
OD2 N:ASP442 4.3 36.6 1.0
N N:ASP442 4.3 36.8 1.0
CA N:LEU41 4.3 37.6 1.0
OD1 N:ASP442 4.3 35.0 1.0
N N:LEU47 4.4 58.4 1.0
CD2 N:LEU41 4.5 31.8 1.0
C N:THR46 4.5 57.8 1.0
N N:GLY45 4.6 43.9 1.0
CA N:SER441 4.6 42.3 1.0
CA N:GLY45 4.7 43.5 1.0
CB N:THR46 4.8 61.3 1.0
OG1 N:THR46 4.9 69.2 1.0
CB N:SER441 4.9 49.3 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: Thu Oct 29 04:09:43 2020

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