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Zinc in PDB 3ag2: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K, PDB code: 3ag2 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.834, 206.933, 178.090, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.3

Other elements in 3ag2:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K 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 Carbon Monoxide-Bound Fully Reduced State at 100 K (pdb code 3ag2). 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 Carbon Monoxide-Bound Fully Reduced State at 100 K, PDB code: 3ag2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ag2

Go back to Zinc Binding Sites List in 3ag2
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K


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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:32.2
occ:1.00
SG F:CYS60 2.3 33.3 1.0
SG F:CYS82 2.3 30.4 1.0
SG F:CYS62 2.3 32.1 1.0
SG F:CYS85 2.4 34.4 1.0
CB F:CYS82 3.2 31.1 1.0
CB F:CYS62 3.3 32.3 1.0
CB F:CYS60 3.4 29.7 1.0
CB F:CYS85 3.4 35.0 1.0
CA F:CYS62 3.6 35.5 1.0
N F:CYS85 3.7 33.9 1.0
CA F:CYS85 4.1 34.7 1.0
N F:CYS62 4.2 35.0 1.0
O F:CYS60 4.4 30.5 1.0
C F:CYS60 4.4 29.5 1.0
CA F:CYS60 4.5 28.1 1.0
O F:HOH2514 4.6 42.5 1.0
CB F:SER84 4.6 31.3 1.0
CA F:CYS82 4.6 31.1 1.0
OG F:SER84 4.7 35.5 1.0
C F:SER84 4.7 34.5 1.0
C F:CYS85 4.8 36.1 1.0
C F:ILE61 4.9 35.5 1.0
C F:CYS62 4.9 37.9 1.0
CG2 F:THR87 4.9 41.5 1.0
OG1 F:THR87 4.9 42.2 1.0
CA F:SER84 5.0 33.3 1.0
CB F:ILE70 5.0 26.7 1.0

Zinc binding site 2 out of 2 in 3ag2

Go back to Zinc Binding Sites List in 3ag2
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K


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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn99

b:35.4
occ:1.00
SG S:CYS60 2.3 31.5 1.0
SG S:CYS62 2.4 34.0 1.0
SG S:CYS82 2.4 35.2 1.0
SG S:CYS85 2.4 36.3 1.0
CB S:CYS82 3.1 31.2 1.0
CB S:CYS62 3.3 36.2 1.0
CB S:CYS60 3.5 34.0 1.0
CB S:CYS85 3.5 37.5 1.0
CA S:CYS62 3.6 38.1 1.0
N S:CYS85 3.7 35.8 1.0
N S:CYS62 4.0 38.0 1.0
CA S:CYS85 4.2 35.3 1.0
O S:CYS60 4.4 32.2 1.0
C S:CYS60 4.4 33.8 1.0
O S:HOH3514 4.5 62.0 1.0
CA S:CYS60 4.5 32.7 1.0
CG2 S:THR87 4.6 40.9 1.0
CA S:CYS82 4.6 32.0 1.0
CB S:SER84 4.6 36.2 1.0
C S:SER84 4.7 36.5 1.0
OG S:SER84 4.7 37.9 1.0
C S:ILE61 4.8 37.2 1.0
C S:CYS85 4.9 37.1 1.0
CB S:ILE70 4.9 29.6 1.0
C S:CYS62 4.9 39.9 1.0
N S:SER84 4.9 36.7 1.0
N S:GLY86 5.0 37.6 1.0
CA S:SER84 5.0 35.5 1.0

Reference:

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Wed Dec 16 04:07:02 2020

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