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Magnesium in PDB 6jy3: Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

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

Protein crystallography data

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 6jy3 was solved by K.Shinzawa-Itoh, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.529, 152.131, 174.083, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 19.2

Other elements in 6jy3:

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Iron (Fe) 2 atoms
Copper (Cu) 3 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 6jy3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 6jy3:

Magnesium binding site 1 out of 1 in 6jy3

Go back to Magnesium Binding Sites List in 6jy3
Magnesium binding site 1 out of 1 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in 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 Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:31.9
occ:1.00
 NE2 A:HIS368 2.1 26.3 1.0
OE1 B:GLU198 2.1 34.6 1.0
OD1 A:ASP369 2.1 29.9 1.0
O B:HOH403 2.2 27.9 1.0
O B:HOH505 2.2 27.6 1.0
O B:HOH443 2.2 27.8 1.0
CD B:GLU198 3.1 31.4 1.0
CE1 A:HIS368 3.1 25.3 1.0
CD2 A:HIS368 3.1 29.8 1.0
CG A:ASP369 3.3 33.6 1.0
OE2 B:GLU198 3.4 31.9 1.0
O B:SER197 3.9 29.4 1.0
O A:HOH843 3.9 26.9 1.0
CB A:ASP369 4.0 31.3 1.0
ND1 A:HIS368 4.2 26.1 1.0
CG A:HIS368 4.2 25.6 1.0
O A:HOH757 4.3 28.0 1.0
OD2 B:ASP173 4.3 30.8 1.0
OD2 A:ASP369 4.3 30.0 1.0
OD1 B:ASP173 4.3 32.0 1.0
CG B:GLU198 4.4 29.5 1.0
OG1 A:THR294 4.5 31.8 1.0
O A:HOH827 4.5 28.9 1.0
O A:HOH866 4.5 26.9 1.0
O A:HOH732 4.6 28.4 1.0
O B:HOH502 4.6 29.3 0.6
CB B:GLU198 4.6 25.8 1.0
CG B:ASP173 4.7 32.8 1.0
O B:HOH452 4.7 37.8 0.4
CA B:GLU198 5.0 29.2 1.0
C B:SER197 5.0 31.8 1.0

Reference:

K.Shinzawa-Itoh, T.Sugimura, T.Misaki, Y.Tadehara, S.Yamamoto, M.Hanada, N.Yano, T.Nakagawa, S.Uene, T.Yamada, H.Aoyama, E.Yamashita, T.Tsukihara, S.Yoshikawa, K.Muramoto. Monomeric Structure of An Active Form of Bovine Cytochromecoxidase. Proc.Natl.Acad.Sci.Usa V. 116 19945 2019.
ISSN: ESSN 1091-6490
PubMed: 31533957
DOI: 10.1073/PNAS.1907183116
Page generated: Wed Aug 13 10:09:23 2025

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