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Zinc in PDB 5xdx: Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, 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 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.044, 205.691, 177.797, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.3

Other elements in 5xdx:

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution (pdb code 5xdx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5xdx

Go back to Zinc Binding Sites List in 5xdx
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:39.9
occ:1.00
SG F:CYS85 2.4 39.9 1.0
SG F:CYS60 2.4 38.8 1.0
SG F:CYS62 2.4 38.6 1.0
SG F:CYS82 2.4 36.7 1.0
CB F:CYS82 3.2 38.3 1.0
CB F:CYS60 3.3 37.5 1.0
CB F:CYS85 3.4 38.9 1.0
CB F:CYS62 3.4 39.1 1.0
CA F:CYS62 3.6 41.1 1.0
N F:CYS85 3.7 40.6 1.0
CA F:CYS85 4.1 39.9 1.0
N F:CYS62 4.1 39.2 1.0
O F:CYS60 4.4 35.4 1.0
C F:CYS60 4.4 36.4 1.0
O F:HOH220 4.5 53.9 1.0
CA F:CYS60 4.5 35.7 1.0
CB F:SER84 4.5 39.9 1.0
OG1 F:THR87 4.6 52.5 1.0
CA F:CYS82 4.6 38.6 1.0
OG F:SER84 4.7 42.7 1.0
C F:SER84 4.7 40.4 1.0
C F:CYS85 4.9 40.2 1.0
C F:ILE61 4.9 39.4 1.0
CB F:ILE70 4.9 32.9 1.0
N F:GLY86 5.0 40.0 1.0
CA F:SER84 5.0 40.0 1.0
CG1 F:ILE70 5.0 31.7 1.0
C F:CYS62 5.0 42.7 1.0

Zinc binding site 2 out of 2 in 5xdx

Go back to Zinc Binding Sites List in 5xdx
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:46.2
occ:1.00
SG S:CYS85 2.4 43.6 1.0
SG S:CYS60 2.4 43.5 1.0
SG S:CYS82 2.4 43.2 1.0
SG S:CYS62 2.4 45.0 1.0
CB S:CYS82 3.2 44.0 1.0
CB S:CYS60 3.3 44.3 1.0
CB S:CYS62 3.4 47.0 1.0
CB S:CYS85 3.4 44.6 1.0
CA S:CYS62 3.6 48.5 1.0
N S:CYS85 3.7 45.5 1.0
N S:CYS62 4.1 46.3 1.0
CA S:CYS85 4.1 45.2 1.0
CB S:SER84 4.4 46.4 1.0
O S:CYS60 4.4 43.4 1.0
C S:CYS60 4.4 43.7 1.0
CA S:CYS60 4.5 44.1 1.0
CG2 S:THR87 4.5 48.9 1.0
OG S:SER84 4.6 45.8 1.0
CA S:CYS82 4.7 45.1 1.0
C S:SER84 4.7 46.2 1.0
C S:ILE61 4.9 46.3 1.0
C S:CYS85 4.9 45.9 1.0
CA S:SER84 4.9 45.9 1.0
CB S:ILE70 4.9 40.4 1.0
CG1 S:ILE70 4.9 39.9 1.0
N S:GLY86 4.9 46.9 1.0
N S:SER84 4.9 47.1 1.0

Reference:

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase in the Ligand-Free Reduced State at Neutral pH. Acta Crystallogr F Struct V. 74 92 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29400318
DOI: 10.1107/S2053230X17018532
Page generated: Wed Dec 16 11:20:02 2020

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