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Magnesium in PDB 1v54: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1v54 was solved by T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.7

Other elements in 1v54:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State 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 Fully Oxidized State (pdb code 1v54). 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 Fully Oxidized State, PDB code: 1v54:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1v54

Go back to Magnesium Binding Sites List in 1v54
Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


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 Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3518

b:21.7
occ:1.00
OD1 A:ASP369 2.0 19.8 1.0
OE1 B:GLU198 2.1 25.7 1.0
NE2 A:HIS368 2.2 15.9 1.0
O B:HOH4092 2.3 19.6 1.0
O B:HOH4093 2.3 24.2 1.0
O B:HOH4091 2.3 22.4 1.0
CE1 A:HIS368 3.1 15.9 1.0
CD2 A:HIS368 3.2 17.5 1.0
CG A:ASP369 3.2 23.2 1.0
CD B:GLU198 3.3 29.5 1.0
O B:SER197 3.8 21.3 1.0
O A:HOH3547 3.9 24.6 1.0
OE2 B:GLU198 3.9 33.4 1.0
CB A:ASP369 4.0 18.0 1.0
OD2 A:ASP369 4.2 24.0 1.0
ND1 A:HIS368 4.3 15.2 1.0
OD2 B:ASP173 4.3 27.2 1.0
O A:HOH3550 4.3 18.9 1.0
CG A:HIS368 4.3 16.2 1.0
OD1 B:ASP173 4.4 21.8 1.0
O A:HOH3532 4.4 18.6 1.0
CG B:GLU198 4.4 21.9 1.0
OG1 A:THR294 4.6 22.5 1.0
CB B:GLU198 4.6 20.0 1.0
O A:HOH3541 4.6 19.5 1.0
O A:HOH3538 4.7 20.6 1.0
CG B:ASP173 4.7 26.2 1.0
CA B:GLU198 4.8 20.1 1.0
C B:SER197 5.0 22.2 1.0
O B:HOH4098 5.0 42.5 1.0

Magnesium binding site 2 out of 2 in 1v54

Go back to Magnesium Binding Sites List in 1v54
Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


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 Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg4518

b:26.8
occ:1.00
OE1 O:GLU198 2.0 32.7 1.0
OD1 N:ASP369 2.1 27.2 1.0
NE2 N:HIS368 2.2 22.2 1.0
O O:HOH1031 2.3 26.2 1.0
O O:HOH1033 2.3 27.8 1.0
O O:HOH1032 2.3 27.5 1.0
CD2 N:HIS368 3.2 20.4 1.0
CD O:GLU198 3.2 32.4 1.0
CE1 N:HIS368 3.2 21.3 1.0
CG N:ASP369 3.3 29.3 1.0
OE2 O:GLU198 3.7 31.8 1.0
O O:SER197 3.9 27.0 1.0
O N:HOH1035 3.9 27.7 1.0
CB N:ASP369 4.0 24.8 1.0
OD2 N:ASP369 4.2 29.9 1.0
OD2 O:ASP173 4.3 33.8 1.0
ND1 N:HIS368 4.3 21.0 1.0
CG N:HIS368 4.3 19.7 1.0
O N:HOH1038 4.3 20.3 1.0
CG O:GLU198 4.4 25.8 1.0
O N:HOH1010 4.4 21.2 1.0
OD1 O:ASP173 4.5 28.2 1.0
OG1 N:THR294 4.5 24.9 1.0
O N:HOH1023 4.5 22.1 1.0
CB O:GLU198 4.6 22.8 1.0
O N:HOH1020 4.7 21.4 1.0
CG O:ASP173 4.8 33.0 1.0
CA O:GLU198 4.9 21.8 1.0
C O:SER197 5.0 26.0 1.0

Reference:

T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa. The Low-Spin Heme of Cytochrome C Oxidase As the Driving Element of the Proton-Pumping Process. Proc.Natl.Acad.Sci.Usa V. 100 15304 2003.
ISSN: ISSN 0027-8424
PubMed: 14673090
DOI: 10.1073/PNAS.2635097100
Page generated: Mon Dec 14 06:54:01 2020

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