Magnesium 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:

Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6j8m

Go back to Magnesium Binding Sites List in 6j8m
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg604

b:29.6
occ:1.00
OD2 A:ASP369 2.0 25.3 1.0
OE1 B:GLU198 2.0 31.2 1.0
O B:HOH428 2.1 27.4 1.0
O B:HOH447 2.2 26.7 1.0
NE2 A:HIS368 2.2 24.9 1.0
O B:HOH543 2.2 26.5 1.0
CD B:GLU198 3.1 30.4 1.0
CE1 A:HIS368 3.1 24.9 1.0
CD2 A:HIS368 3.1 24.4 1.0
CG A:ASP369 3.2 28.0 1.0
OE2 B:GLU198 3.5 29.7 1.0
O B:SER197 3.8 26.7 1.0
CB A:ASP369 3.9 28.2 1.0
O A:HOH899 4.0 27.8 1.0
OD1 A:ASP369 4.1 25.3 1.0
OD1 B:ASP173 4.2 27.1 1.0
O A:HOH855 4.2 24.3 1.0
ND1 A:HIS368 4.2 25.0 1.0
CG A:HIS368 4.3 25.8 1.0
OD2 B:ASP173 4.3 27.8 1.0
CG B:GLU198 4.4 27.5 1.0
OG1 A:THR294 4.4 28.5 1.0
O A:HOH703 4.5 26.3 1.0
O A:HOH821 4.5 28.7 1.0
O B:HOH545 4.5 37.4 1.0
CB B:GLU198 4.6 28.1 1.0
CG B:ASP173 4.7 28.3 1.0
O A:HOH881 4.7 24.9 1.0
CA B:GLU198 4.8 29.2 1.0
CA A:ASP369 5.0 27.1 1.0
C B:SER197 5.0 29.1 1.0

Magnesium binding site 2 out of 2 in 6j8m

Go back to Magnesium Binding Sites List in 6j8m
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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
N:Mg604

b:36.1
occ:1.00
OD2 N:ASP369 2.0 30.4 1.0
OE1 O:GLU198 2.0 36.9 1.0
O O:HOH410 2.1 32.9 1.0
NE2 N:HIS368 2.1 30.9 1.0
O O:HOH471 2.1 31.6 1.0
O O:HOH512 2.2 30.2 1.0
CD2 N:HIS368 3.1 28.9 1.0
CD O:GLU198 3.1 33.8 1.0
CE1 N:HIS368 3.1 29.0 1.0
CG N:ASP369 3.2 32.8 1.0
OE2 O:GLU198 3.5 32.1 1.0
O O:SER197 3.9 31.7 1.0
O N:HOH884 3.9 32.1 1.0
CB N:ASP369 3.9 32.4 1.0
OD1 N:ASP369 4.2 32.5 1.0
ND1 N:HIS368 4.2 28.2 1.0
CG N:HIS368 4.2 29.7 1.0
O N:HOH813 4.2 24.9 1.0
OD2 O:ASP173 4.2 32.9 1.0
OD1 O:ASP173 4.3 32.3 1.0
CG O:GLU198 4.4 32.8 1.0
OG1 N:THR294 4.4 33.4 1.0
O N:HOH702 4.5 27.6 1.0
O N:HOH878 4.6 26.8 1.0
O N:HOH869 4.6 30.7 1.0
O O:HOH522 4.6 47.4 1.0
CB O:GLU198 4.7 30.4 1.0
CG O:ASP173 4.7 31.0 1.0
CA O:GLU198 4.9 31.9 1.0
CA N:ASP369 4.9 31.3 1.0
C O:SER197 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: Mon Dec 14 23:00:23 2020

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