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Magnesium in PDB 3ag1: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K, PDB code: 3ag1 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.493, 210.887, 178.301, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.2

Other elements in 3ag1:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K 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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K (pdb code 3ag1). 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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K, PDB code: 3ag1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ag1

Go back to Magnesium Binding Sites List in 3ag1
Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K


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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg518

b:40.4
occ:1.00
OD1 A:ASP369 2.1 34.9 1.0
NE2 A:HIS368 2.1 40.4 1.0
OE1 B:GLU198 2.2 39.7 1.0
O B:HOH2266 2.3 38.4 1.0
O B:HOH2267 2.3 40.0 1.0
O B:HOH2268 2.3 37.3 1.0
CE1 A:HIS368 3.1 38.3 1.0
CD2 A:HIS368 3.1 41.9 1.0
CG A:ASP369 3.3 42.4 1.0
CD B:GLU198 3.4 42.5 1.0
O A:HOH2278 3.9 36.6 1.0
O B:SER197 3.9 40.7 1.0
CB A:ASP369 4.0 36.6 1.0
O A:HOH2116 4.1 40.1 1.0
OE2 B:GLU198 4.2 44.0 1.0
ND1 A:HIS368 4.2 38.9 1.0
OD2 A:ASP369 4.2 41.3 1.0
CG A:HIS368 4.2 40.9 1.0
OD2 B:ASP173 4.2 48.7 1.0
O B:HOH2475 4.3 38.8 1.0
O A:HOH2297 4.3 39.4 1.0
OD1 B:ASP173 4.4 41.4 1.0
CB B:GLU198 4.4 39.7 1.0
CG B:GLU198 4.4 42.0 1.0
O A:HOH2209 4.5 39.2 1.0
OG1 A:THR294 4.6 44.1 1.0
O A:HOH2219 4.7 37.8 1.0
CG B:ASP173 4.7 44.0 1.0
CA B:GLU198 4.8 38.9 1.0

Magnesium binding site 2 out of 2 in 3ag1

Go back to Magnesium Binding Sites List in 3ag1
Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K


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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg518

b:50.1
occ:1.00
NE2 N:HIS368 2.1 51.1 1.0
OD1 N:ASP369 2.1 50.8 1.0
OE1 O:GLU198 2.2 54.8 1.0
O O:HOH3266 2.3 50.6 1.0
O O:HOH3268 2.3 48.2 1.0
O O:HOH3267 2.4 44.3 1.0
CD2 N:HIS368 2.9 43.4 1.0
CE1 N:HIS368 3.1 47.7 1.0
CG N:ASP369 3.2 48.2 1.0
CD O:GLU198 3.4 53.6 1.0
O O:SER197 3.7 54.2 1.0
CB N:ASP369 3.9 48.2 1.0
CG N:HIS368 4.1 50.5 1.0
OD2 N:ASP369 4.1 53.2 1.0
O N:HOH3278 4.2 44.9 1.0
ND1 N:HIS368 4.2 51.8 1.0
OD2 O:ASP173 4.2 52.8 1.0
O N:HOH3116 4.2 47.3 1.0
OE2 O:GLU198 4.3 51.0 1.0
OD1 O:ASP173 4.4 52.1 1.0
CB O:GLU198 4.4 49.0 1.0
CG O:GLU198 4.4 47.5 1.0
OG1 N:THR294 4.5 50.4 1.0
O N:HOH3219 4.6 48.1 1.0
O N:HOH3297 4.6 47.1 1.0
O O:HOH3475 4.6 46.0 1.0
CG O:ASP173 4.7 53.5 1.0
CA O:GLU198 4.8 51.0 1.0
C O:SER197 4.8 53.8 1.0
O N:HOH3209 4.9 53.7 1.0
CA N:ASP369 5.0 49.2 1.0

Reference:

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Mon Dec 14 07:53:09 2020

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