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Zinc in PDB 1oco: Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State, PDB code: 1oco was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.6

Other elements in 1oco:

The structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State (pdb code 1oco). 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 Carbon Monoxide-Bound State, PDB code: 1oco:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1oco

Go back to Zinc Binding Sites List in 1oco
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State


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 Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:20.7
occ:1.00
SG F:CYS85 2.1 20.8 1.0
SG F:CYS82 2.2 16.7 1.0
SG F:CYS62 2.2 25.7 1.0
SG F:CYS60 2.2 23.5 1.0
CB F:CYS82 2.9 22.7 1.0
CB F:CYS60 3.2 14.8 1.0
CB F:CYS62 3.5 14.3 1.0
CB F:CYS85 3.6 12.5 1.0
CA F:CYS62 3.7 21.1 1.0
N F:CYS62 3.9 20.2 1.0
N F:CYS85 4.0 22.8 1.0
OG F:SER84 4.0 43.0 1.0
CA F:CYS85 4.3 21.0 1.0
O F:CYS60 4.3 27.4 1.0
C F:CYS60 4.4 20.3 1.0
CA F:CYS60 4.4 12.9 1.0
CA F:CYS82 4.4 18.0 1.0
CB F:THR87 4.7 19.3 1.0
OG1 F:THR87 4.7 24.7 1.0
C F:SER84 4.9 25.6 1.0
C F:ILE61 4.9 21.6 1.0
C F:CYS85 4.9 25.4 1.0
OH F:TYR89 5.0 15.6 1.0
N F:ILE61 5.0 22.7 1.0
C F:CYS82 5.0 19.6 1.0

Zinc binding site 2 out of 2 in 1oco

Go back to Zinc Binding Sites List in 1oco
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State


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 Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn99

b:30.1
occ:1.00
SG S:CYS85 2.1 35.1 1.0
SG S:CYS60 2.2 26.5 1.0
SG S:CYS62 2.2 27.9 1.0
SG S:CYS82 2.2 31.8 1.0
CB S:CYS82 2.9 29.0 1.0
CB S:CYS60 3.2 19.8 1.0
CB S:CYS62 3.5 16.8 1.0
CB S:CYS85 3.6 37.9 1.0
CA S:CYS62 3.7 25.8 1.0
N S:CYS62 4.0 25.6 1.0
N S:CYS85 4.0 35.9 1.0
OG S:SER84 4.2 38.1 1.0
CA S:CYS85 4.3 34.3 1.0
CA S:CYS82 4.4 25.4 1.0
CA S:CYS60 4.4 18.8 1.0
C S:CYS60 4.5 23.8 1.0
O S:CYS60 4.6 23.3 1.0
CB S:THR87 4.6 27.2 1.0
OG1 S:THR87 4.6 31.9 1.0
C S:CYS85 4.8 35.5 1.0
OH S:TYR89 4.9 34.7 1.0
C S:SER84 4.9 40.1 1.0
C S:ILE61 4.9 25.3 1.0
C S:CYS82 5.0 23.4 1.0

Reference:

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723
Page generated: Mon Jan 25 16:11:03 2021

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