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Magnesium 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:

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 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K), PDB code: 3abk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3abk

Go back to Magnesium Binding Sites List in 3abk
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg518

b:23.8
occ:1.00
OD1 A:ASP369 2.1 25.6 1.0
NE2 A:HIS368 2.1 17.1 1.0
OE1 B:GLU198 2.2 22.5 1.0
O B:HOH2266 2.2 27.3 1.0
O B:HOH2268 2.2 26.7 1.0
O A:HOH2267 2.3 24.9 1.0
CE1 A:HIS368 3.0 21.1 1.0
CD2 A:HIS368 3.2 28.0 1.0
CG A:ASP369 3.3 28.0 1.0
CD B:GLU198 3.4 38.4 1.0
O B:SER197 3.9 26.5 1.0
O A:HOH2278 4.0 23.7 1.0
O A:HOH2116 4.1 25.5 1.0
CB A:ASP369 4.1 24.5 1.0
OD2 A:ASP369 4.2 26.1 1.0
ND1 A:HIS368 4.2 17.9 1.0
OD2 B:ASP173 4.2 27.9 1.0
CG A:HIS368 4.3 16.9 1.0
O A:HOH2475 4.3 27.8 1.0
OE2 B:GLU198 4.3 31.0 1.0
CG B:GLU198 4.3 23.3 1.0
OD1 B:ASP173 4.3 29.1 1.0
O A:HOH2297 4.3 24.9 1.0
CB B:GLU198 4.3 23.7 1.0
O A:HOH2209 4.6 24.6 1.0
CA B:GLU198 4.6 25.5 1.0
OG1 A:THR294 4.6 24.4 1.0
CG B:ASP173 4.7 30.6 1.0
O A:HOH2219 4.7 26.6 1.0
O B:HOH2480 4.7 40.4 1.0
C B:SER197 5.0 28.1 1.0

Magnesium binding site 2 out of 2 in 3abk

Go back to Magnesium Binding Sites List in 3abk
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg518

b:34.6
occ:1.00
NE2 N:HIS368 2.1 27.1 1.0
OD1 N:ASP369 2.2 35.9 1.0
OE1 O:GLU198 2.2 31.1 1.0
O O:HOH3266 2.3 39.1 1.0
O N:HOH3267 2.3 31.2 1.0
O O:HOH3268 2.3 36.1 1.0
CE1 N:HIS368 3.0 30.3 1.0
CD2 N:HIS368 3.2 32.0 1.0
CG N:ASP369 3.4 37.6 1.0
CD O:GLU198 3.4 39.9 1.0
O O:SER197 3.8 34.2 1.0
O N:HOH3278 4.0 29.8 1.0
CB N:ASP369 4.1 32.3 1.0
O N:HOH3116 4.2 30.0 1.0
ND1 N:HIS368 4.2 24.8 1.0
OE2 O:GLU198 4.2 36.4 1.0
OD2 O:ASP173 4.2 41.5 1.0
OD2 N:ASP369 4.2 37.3 1.0
O O:HOH3475 4.3 39.7 1.0
CB O:GLU198 4.3 35.0 1.0
CG N:HIS368 4.3 28.9 1.0
O N:HOH3297 4.3 31.4 1.0
OD1 O:ASP173 4.3 38.7 1.0
CG O:GLU198 4.4 31.8 1.0
CA O:GLU198 4.6 33.5 1.0
OG1 N:THR294 4.6 30.3 1.0
O N:HOH3219 4.7 31.6 1.0
CG O:ASP173 4.7 38.9 1.0
O N:HOH3209 4.7 31.7 1.0
C O:SER197 4.9 35.5 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: Mon Dec 14 07:52:53 2020

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