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Sodium in PDB 6j8m: Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray

Enzymatic activity of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray

All present enzymatic activity of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray:
1.9.3.1;

Protein crystallography data

The structure of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray, PDB code: 6j8m was solved by G.Ueno, A.Shimada, E.Yamashita, K.Hasegawa, T.Kumasaka, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, M.Yamamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.020, 203.540, 177.410, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.9

Other elements in 6j8m:

The structure of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray 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 Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray (pdb code 6j8m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray, PDB code: 6j8m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6j8m

Go back to Sodium Binding Sites List in 6j8m
Sodium binding site 1 out of 4 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:30.9
occ:1.00
 O A:HOH827 2.2 31.4 1.0
O A:SER441 2.3 31.3 1.0
O A:GLY45 2.3 33.3 1.0
OE1 A:GLU40 2.3 29.9 1.0
O A:GLU40 2.5 30.6 1.0
CD A:GLU40 3.3 31.4 1.0
O A:HOH730 3.4 41.7 1.0
C A:GLU40 3.4 31.8 1.0
CG A:GLU40 3.5 31.5 1.0
C A:GLY45 3.5 34.8 1.0
C A:SER441 3.5 32.7 1.0
O A:GLN43 3.9 31.4 1.0
CA A:ASP442 4.0 31.3 1.0
CB A:ASP442 4.0 29.8 1.0
OD1 A:ASP442 4.1 30.6 1.0
CA A:THR46 4.1 35.5 1.0
CG A:ASP442 4.2 32.9 1.0
N A:THR46 4.2 34.5 1.0
N A:ASP442 4.2 30.5 1.0
CA A:GLU40 4.3 32.2 1.0
N A:LEU41 4.3 30.1 1.0
N A:GLY45 4.4 33.6 1.0
CA A:LEU41 4.4 29.2 1.0
N A:LEU47 4.4 34.4 1.0
OE2 A:GLU40 4.4 33.2 1.0
CB A:GLU40 4.5 29.6 1.0
CA A:GLY45 4.6 33.9 1.0
CA A:SER441 4.6 31.2 1.0
CD2 A:LEU41 4.7 29.4 1.0
C A:THR46 4.7 37.7 1.0
OD2 A:ASP442 5.0 31.9 1.0
C A:PRO44 5.0 35.2 1.0
CB A:SER441 5.0 29.8 1.0

Sodium binding site 2 out of 4 in 6j8m

Go back to Sodium Binding Sites List in 6j8m
Sodium binding site 2 out of 4 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:49.2
occ:1.00
 NE2 C:HIS148 2.5 40.1 1.0
NE2 C:HIS232 2.7 32.6 1.0
O C:HOH529 3.1 71.3 1.0
CE1 C:HIS148 3.3 43.5 1.0
CD2 C:HIS232 3.5 34.3 1.0
CD2 C:HIS148 3.6 41.0 1.0
CD C:GLU236 3.6 43.3 1.0
SD C:MET152 3.7 41.6 1.0
CE1 C:HIS232 3.7 34.1 1.0
CG C:MET152 3.8 35.0 1.0
OE1 C:GLU236 3.9 43.8 1.0
OE2 C:GLU236 3.9 44.6 1.0
CG C:GLU236 3.9 39.7 1.0
ND1 C:HIS148 4.5 41.8 1.0
CG C:HIS148 4.7 39.7 1.0
CG C:HIS232 4.7 32.8 1.0
CE C:MET152 4.7 34.4 1.0
ND1 C:HIS232 4.8 33.3 1.0

Sodium binding site 3 out of 4 in 6j8m

Go back to Sodium Binding Sites List in 6j8m
Sodium binding site 3 out of 4 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:35.7
occ:1.00
 OE1 N:GLU40 2.3 35.2 1.0
O N:SER441 2.3 36.2 1.0
O N:GLY45 2.3 39.1 1.0
O N:GLU40 2.4 34.0 1.0
O N:HOH822 2.4 36.0 1.0
CD N:GLU40 3.2 37.2 1.0
O N:HOH759 3.3 40.6 1.0
C N:GLU40 3.3 34.3 1.0
CG N:GLU40 3.5 34.4 1.0
C N:SER441 3.5 34.3 1.0
C N:GLY45 3.5 42.1 1.0
O N:GLN43 3.9 37.8 1.0
CA N:THR46 4.1 43.5 1.0
CA N:ASP442 4.1 36.1 1.0
CA N:GLU40 4.1 35.2 1.0
OD1 N:ASP442 4.2 37.4 1.0
N N:LEU41 4.2 34.1 1.0
N N:THR46 4.2 42.6 1.0
CB N:ASP442 4.2 35.8 1.0
N N:ASP442 4.2 34.8 1.0
CG N:ASP442 4.3 38.3 1.0
N N:LEU47 4.3 45.4 1.0
CB N:GLU40 4.4 34.5 1.0
CA N:LEU41 4.4 34.0 1.0
OE2 N:GLU40 4.4 38.0 1.0
N N:GLY45 4.5 38.2 1.0
CA N:SER441 4.5 35.7 1.0
CD2 N:LEU41 4.6 32.1 1.0
CA N:GLY45 4.6 39.9 1.0
C N:THR46 4.6 45.1 1.0
CB N:SER441 4.8 35.4 1.0
OD2 N:ASP442 5.0 37.2 1.0

Sodium binding site 4 out of 4 in 6j8m

Go back to Sodium Binding Sites List in 6j8m
Sodium binding site 4 out of 4 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na301

b:47.5
occ:1.00
 NE2 P:HIS148 2.7 41.4 1.0
NE2 P:HIS232 2.8 31.9 1.0
CE1 P:HIS148 3.5 44.3 1.0
CD P:GLU236 3.6 49.5 1.0
CD2 P:HIS232 3.7 30.8 1.0
CD2 P:HIS148 3.7 38.8 1.0
CE1 P:HIS232 3.8 31.4 1.0
SD P:MET152 3.8 42.4 1.0
OE1 P:GLU236 3.8 50.5 1.0
OE2 P:GLU236 3.8 50.0 1.0
CG P:GLU236 3.9 43.4 1.0
CG P:MET152 4.0 36.0 1.0
O P:HOH512 4.5 66.8 1.0
O P:HOH436 4.5 55.2 1.0
ND1 P:HIS148 4.7 41.5 1.0
CG P:HIS148 4.8 38.1 1.0
CG P:HIS232 4.8 31.0 1.0
ND1 P:HIS232 4.8 30.8 1.0
O P:HOH452 5.0 31.6 1.0
CE P:MET152 5.0 33.7 1.0

Reference:

G.Ueno, A.Shimada, E.Yamashita, K.Hasegawa, T.Kumasaka, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, M.Yamamoto. Low-Dose X-Ray Structure Analysis of Cytochrome C Oxidase Utilizing High-Energy X-Rays. J.Synchrotron Radiat. V. 26 912 2019.
ISSN: ESSN 1600-5775
PubMed: 31274413
DOI: 10.1107/S1600577519006805
Page generated: Tue Oct 8 11:23:33 2024

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