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Magnesium in PDB 3x2q: X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution

Enzymatic activity of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution

All present enzymatic activity of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution, PDB code: 3x2q was solved by N.Yano, K.Muramoto, M.Mochizuki, 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 (°) 183.678, 206.675, 178.201, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.4

Other elements in 3x2q:

The structure of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution (pdb code 3x2q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution, PDB code: 3x2q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3x2q

Go back to Magnesium Binding Sites List in 3x2q
Magnesium binding site 1 out of 2 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:28.0
occ:1.00
 OD1 A:ASP369 2.0 28.1 1.0
NE2 A:HIS368 2.1 24.4 1.0
OE1 B:GLU198 2.2 30.8 1.0
O B:HOH430 2.2 26.7 1.0
O A:HOH760 2.2 25.1 1.0
O B:HOH429 2.3 26.9 1.0
CE1 A:HIS368 3.0 23.4 1.0
CD2 A:HIS368 3.1 26.4 1.0
CG A:ASP369 3.2 23.7 1.0
CD B:GLU198 3.2 32.1 1.0
OE2 B:GLU198 3.5 34.3 1.0
O B:SER197 3.8 24.5 1.0
O A:HOH762 3.9 30.0 1.0
CB A:ASP369 4.0 25.6 1.0
ND1 A:HIS368 4.2 24.6 1.0
CG A:HIS368 4.2 24.6 1.0
OD2 A:ASP369 4.2 32.0 1.0
OD1 B:ASP173 4.2 30.8 1.0
OD2 B:ASP173 4.2 31.5 1.0
O A:HOH763 4.2 24.5 1.0
O A:HOH754 4.4 24.1 1.0
OG1 A:THR294 4.4 27.4 1.0
CG B:GLU198 4.5 25.2 1.0
O A:HOH759 4.6 26.9 1.0
O B:HOH435 4.6 41.0 1.0
CB B:GLU198 4.6 22.5 1.0
CG B:ASP173 4.6 28.0 1.0
O A:HOH757 4.7 28.0 1.0
O A:HOH768 4.9 36.4 1.0
CA B:GLU198 4.9 24.2 1.0
C B:SER197 5.0 27.3 1.0

Magnesium binding site 2 out of 2 in 3x2q

Go back to Magnesium Binding Sites List in 3x2q
Magnesium binding site 2 out of 2 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg605

b:39.9
occ:1.00
 OD1 N:ASP369 1.9 38.0 1.0
NE2 N:HIS368 2.1 36.0 1.0
OE1 O:GLU198 2.1 45.8 1.0
O O:HOH431 2.3 39.1 1.0
O O:HOH432 2.3 35.5 1.0
O O:HOH433 2.3 38.3 1.0
CD2 N:HIS368 3.0 34.3 1.0
CE1 N:HIS368 3.1 33.2 1.0
CD O:GLU198 3.1 37.5 1.0
CG N:ASP369 3.2 39.3 1.0
OE2 O:GLU198 3.4 40.4 1.0
O O:SER197 3.7 33.5 1.0
O N:HOH757 3.8 36.6 1.0
CB N:ASP369 3.9 34.6 1.0
OD2 N:ASP369 4.1 38.9 1.0
ND1 N:HIS368 4.2 30.9 1.0
CG N:HIS368 4.2 33.0 1.0
O N:HOH750 4.4 35.0 1.0
O N:HOH758 4.4 32.6 1.0
OD2 O:ASP173 4.4 42.7 1.0
CG O:GLU198 4.5 32.7 1.0
OD1 O:ASP173 4.5 35.4 1.0
OG1 N:THR294 4.5 34.5 1.0
O O:HOH438 4.6 60.2 1.0
CB O:GLU198 4.6 30.4 1.0
O N:HOH755 4.6 31.9 1.0
O N:HOH753 4.7 35.6 1.0
CG O:ASP173 4.8 36.5 1.0
CA O:GLU198 4.9 34.2 1.0
C O:SER197 4.9 35.6 1.0
CA N:ASP369 4.9 34.7 1.0

Reference:

N.Yano, K.Muramoto, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara. X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution. Acta Crystallogr F Struct V. 71 726 2015BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 26057802
DOI: 10.1107/S2053230X15007025
Page generated: Thu Aug 15 13:50:03 2024

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