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Zinc in PDB 1ocr: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 1ocr 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) 15.00 / 2.35
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 (%) 20.3 / 24.7

Other elements in 1ocr:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 the Fully Reduced State (pdb code 1ocr). 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 Fully Reduced State, PDB code: 1ocr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ocr

Go back to Zinc Binding Sites List in 1ocr
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:30.3
occ:1.00
SG F:CYS82 2.1 27.9 1.0
SG F:CYS60 2.1 20.4 1.0
SG F:CYS85 2.2 31.0 1.0
SG F:CYS62 2.2 25.2 1.0
CB F:CYS60 3.0 12.1 1.0
CB F:CYS82 3.0 30.3 1.0
CB F:CYS62 3.5 24.1 1.0
CB F:CYS85 3.6 26.9 1.0
CA F:CYS62 3.7 27.8 1.0
N F:CYS85 3.9 31.4 1.0
N F:CYS62 4.0 25.6 1.0
O F:CYS60 4.0 20.5 1.0
CA F:CYS60 4.2 10.9 1.0
C F:CYS60 4.2 16.8 1.0
CA F:CYS85 4.3 30.1 1.0
CA F:CYS82 4.5 26.1 1.0
CB F:SER84 4.6 37.3 1.0
C F:SER84 4.8 30.4 1.0
C F:ILE61 4.8 25.5 1.0
OG F:SER84 4.9 40.6 1.0
OH F:TYR89 4.9 22.8 1.0
CB F:ILE70 4.9 26.5 1.0
CB F:THR87 4.9 24.8 1.0
N F:ILE61 5.0 23.0 1.0

Zinc binding site 2 out of 2 in 1ocr

Go back to Zinc Binding Sites List in 1ocr
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn99

b:34.6
occ:1.00
SG S:CYS85 2.1 35.5 1.0
SG S:CYS60 2.2 31.5 1.0
SG S:CYS82 2.2 36.8 1.0
SG S:CYS62 2.2 33.7 1.0
CB S:CYS82 2.9 38.5 1.0
CB S:CYS60 3.1 25.9 1.0
CB S:CYS85 3.5 37.3 1.0
CB S:CYS62 3.5 29.2 1.0
CA S:CYS62 3.8 33.7 1.0
N S:CYS85 3.8 37.8 1.0
N S:CYS62 4.1 30.1 1.0
O S:CYS60 4.2 30.3 1.0
CA S:CYS85 4.2 35.8 1.0
CA S:CYS60 4.3 25.4 1.0
C S:CYS60 4.3 28.4 1.0
CA S:CYS82 4.4 36.2 1.0
CB S:SER84 4.6 38.4 1.0
C S:SER84 4.8 38.3 1.0
CB S:THR87 4.9 33.7 1.0
OG S:SER84 4.9 41.1 1.0
OH S:TYR89 4.9 37.0 1.0
CB S:ILE70 4.9 26.6 1.0
C S:ILE61 4.9 30.0 1.0
C S:CYS85 5.0 37.6 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: Wed Dec 16 02:59:32 2020

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