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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy