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Sodium 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:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom
Iron (Fe) 2 atoms
Copper (Cu) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 6jy3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6jy3

Go back to Sodium Binding Sites List in 6jy3
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na605

b:35.7
occ:1.00
O A:GLY45 2.3 39.8 1.0
OE1 A:GLU40 2.3 38.2 1.0
O A:SER441 2.3 32.3 1.0
O A:GLU40 2.3 35.5 1.0
O A:HOH844 2.3 34.7 1.0
CD A:GLU40 3.2 36.5 1.0
O A:HOH816 3.3 46.2 1.0
C A:GLU40 3.3 33.3 1.0
CG A:GLU40 3.4 32.6 1.0
C A:GLY45 3.4 42.3 1.0
C A:SER441 3.5 32.7 1.0
CA A:ASP442 4.0 34.8 1.0
CB A:ASP442 4.1 32.6 1.0
O A:GLN43 4.1 38.3 1.0
OD2 A:ASP442 4.1 38.9 1.0
CA A:THR46 4.1 41.4 1.0
CG A:ASP442 4.2 32.5 1.0
CA A:GLU40 4.2 32.6 1.0
N A:THR46 4.2 41.0 1.0
N A:ASP442 4.2 32.6 1.0
N A:LEU41 4.2 33.1 1.0
N A:LEU47 4.3 37.1 1.0
OE2 A:GLU40 4.3 35.2 1.0
CB A:GLU40 4.4 33.8 1.0
CA A:LEU41 4.4 34.2 1.0
N A:GLY45 4.4 37.1 1.0
CA A:GLY45 4.5 36.4 1.0
CA A:SER441 4.6 31.3 1.0
CD2 A:LEU41 4.7 33.6 1.0
C A:THR46 4.7 40.4 1.0
CB A:SER441 4.9 28.4 1.0
OD1 A:ASP442 4.9 39.0 1.0

Sodium binding site 2 out of 2 in 6jy3

Go back to Sodium Binding Sites List in 6jy3
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na binding site number 2 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
C:Na302

b:64.4
occ:1.00
OE1 C:GLU236 2.2 83.6 1.0
NE2 C:HIS148 2.3 58.5 1.0
NE2 C:HIS232 2.3 45.1 1.0
CD C:GLU236 2.9 61.4 1.0
CD2 C:HIS232 3.0 39.2 1.0
CE1 C:HIS148 3.1 51.4 1.0
CD2 C:HIS148 3.3 46.5 1.0
CG C:GLU236 3.3 42.2 1.0
CE1 C:HIS232 3.4 44.5 1.0
OE2 C:GLU236 3.6 43.2 1.0
CG C:MET152 4.2 49.1 1.0
SD C:MET152 4.2 58.6 1.0
CG C:HIS232 4.3 37.7 1.0
ND1 C:HIS148 4.3 54.4 1.0
ND1 C:HIS232 4.4 40.3 1.0
CG C:HIS148 4.4 39.1 1.0
O C:HOH440 4.7 53.4 1.0
O C:HOH420 4.8 39.1 1.0
CB C:GLU236 4.8 36.1 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: Tue Dec 15 12:25:54 2020

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