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Sodium in PDB 3abk: Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K), PDB code: 3abk was solved by K.Ohta, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, 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 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.247, 207.944, 177.997, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.9

Other elements in 3abk:

The structure of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K) 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 No-Bound Fully Reduced State (50K) (pdb code 3abk). 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 No-Bound Fully Reduced State (50K), PDB code: 3abk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3abk

Go back to Sodium Binding Sites List in 3abk
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na519

b:32.0
occ:1.00
O A:HOH2258 2.2 27.7 1.0
OE1 A:GLU40 2.3 34.6 1.0
O A:GLY45 2.3 33.2 1.0
O A:SER441 2.3 31.8 1.0
O A:GLU40 2.3 32.1 1.0
O A:HOH2563 3.1 41.8 1.0
CD A:GLU40 3.2 36.1 1.0
C A:GLU40 3.4 27.7 1.0
C A:GLY45 3.5 32.6 1.0
C A:SER441 3.5 30.6 1.0
CG A:GLU40 3.5 27.8 1.0
O A:HOH2691 3.8 38.9 1.0
O A:GLN43 3.9 31.7 1.0
CB A:ASP442 3.9 28.4 1.0
CA A:THR46 3.9 35.9 1.0
CA A:ASP442 4.0 30.1 1.0
CG A:ASP442 4.0 30.9 1.0
OD2 A:ASP442 4.1 27.4 1.0
N A:THR46 4.2 33.1 1.0
N A:ASP442 4.2 30.5 1.0
CA A:GLU40 4.2 29.0 1.0
N A:LEU41 4.3 27.2 1.0
CA A:LEU41 4.3 26.0 1.0
OE2 A:GLU40 4.4 34.4 1.0
N A:LEU47 4.4 37.6 1.0
N A:GLY45 4.5 29.8 1.0
C A:THR46 4.5 37.6 1.0
CB A:GLU40 4.5 27.1 1.0
CD2 A:LEU41 4.6 26.1 1.0
CA A:GLY45 4.6 30.0 1.0
CA A:SER441 4.7 29.2 1.0
OD1 A:ASP442 4.7 27.3 1.0
O A:HOH2693 4.9 36.6 1.0

Sodium binding site 2 out of 2 in 3abk

Go back to Sodium Binding Sites List in 3abk
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na519

b:39.4
occ:1.00
O N:HOH3258 2.2 38.5 1.0
OE1 N:GLU40 2.3 35.3 1.0
O N:SER441 2.3 38.0 1.0
O N:GLY45 2.3 43.5 1.0
O N:GLU40 2.3 35.8 1.0
CD N:GLU40 3.3 42.5 1.0
C N:GLU40 3.4 36.0 1.0
C N:SER441 3.4 36.1 1.0
C N:GLY45 3.5 42.9 1.0
O N:HOH3563 3.5 47.5 1.0
CG N:GLU40 3.6 35.6 1.0
CA N:ASP442 3.8 36.9 1.0
O N:HOH3691 3.8 54.5 1.0
O N:GLN43 3.9 41.2 1.0
CB N:ASP442 4.0 37.5 1.0
N N:ASP442 4.1 37.3 1.0
CA N:THR46 4.1 45.7 1.0
OD2 N:ASP442 4.1 36.7 1.0
CG N:ASP442 4.1 39.0 1.0
N N:THR46 4.2 43.7 1.0
N N:LEU41 4.3 35.0 1.0
CA N:LEU41 4.3 36.1 1.0
CA N:GLU40 4.3 35.1 1.0
OE2 N:GLU40 4.4 44.0 1.0
N N:GLY45 4.5 42.0 1.0
CD2 N:LEU41 4.5 31.0 1.0
CB N:GLU40 4.6 36.7 1.0
CA N:GLY45 4.6 40.7 1.0
N N:LEU47 4.6 46.7 1.0
CA N:SER441 4.6 36.0 1.0
C N:THR46 4.8 46.9 1.0
OD1 N:ASP442 4.8 37.2 1.0

Reference:

K.Ohta, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara. X-Ray Structure of the No-Bound Cu(B) in Bovine Cytochrome C Oxidase Acta Crystallogr.,Sect.F V. 66 251 2010.
ISSN: ESSN 1744-3091
PubMed: 20208153
DOI: 10.1107/S1744309109055109
Page generated: Tue Dec 15 06:01:53 2020

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