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Zinc in PDB 3ag1: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 280 K, PDB code: 3ag1 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.493, 210.887, 178.301, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.2

Other elements in 3ag1:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 280 K (pdb code 3ag1). 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 280 K, PDB code: 3ag1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ag1

Go back to Zinc Binding Sites List in 3ag1
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:48.5
occ:1.00
SG F:CYS60 2.3 43.1 1.0
SG F:CYS82 2.3 48.5 1.0
SG F:CYS62 2.4 46.6 1.0
SG F:CYS85 2.4 48.0 1.0
CB F:CYS82 3.1 50.4 1.0
CB F:CYS60 3.2 42.7 1.0
CB F:CYS85 3.4 46.4 1.0
CB F:CYS62 3.4 48.2 1.0
N F:CYS85 3.6 48.8 1.0
CA F:CYS62 3.6 50.7 1.0
CA F:CYS85 4.1 47.0 1.0
N F:CYS62 4.1 49.3 1.0
O F:CYS60 4.3 46.6 1.0
C F:CYS60 4.4 44.3 1.0
CA F:CYS60 4.4 42.6 1.0
O F:HOH2514 4.6 67.0 1.0
CA F:CYS82 4.6 49.1 1.0
CG2 F:THR87 4.6 43.5 1.0
OG F:SER84 4.6 54.5 1.0
C F:SER84 4.7 49.4 1.0
C F:CYS85 4.8 49.1 1.0
CB F:SER84 4.8 50.2 1.0
C F:ILE61 4.9 48.9 1.0
N F:GLY86 4.9 49.9 1.0
N F:SER84 4.9 49.9 1.0
CB F:ILE70 5.0 42.1 1.0
CA F:SER84 5.0 49.8 1.0

Zinc binding site 2 out of 2 in 3ag1

Go back to Zinc Binding Sites List in 3ag1
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn99

b:56.8
occ:1.00
SG S:CYS60 2.3 53.2 1.0
SG S:CYS62 2.4 56.3 1.0
SG S:CYS85 2.4 58.2 1.0
SG S:CYS82 2.4 55.2 1.0
CB S:CYS60 3.2 52.5 1.0
CB S:CYS82 3.2 57.6 1.0
CB S:CYS62 3.3 57.2 1.0
CB S:CYS85 3.4 57.4 1.0
CA S:CYS62 3.6 58.6 1.0
N S:CYS85 3.7 59.4 1.0
N S:CYS62 4.1 55.9 1.0
CA S:CYS85 4.1 58.1 1.0
CA S:CYS60 4.4 52.3 1.0
C S:CYS60 4.4 52.3 1.0
O S:CYS60 4.5 51.8 1.0
CB S:SER84 4.6 60.5 1.0
O S:HOH3514 4.6 81.7 1.0
C S:SER84 4.6 59.4 1.0
CA S:CYS82 4.7 58.2 1.0
C S:CYS85 4.8 58.7 1.0
OG S:SER84 4.9 63.1 1.0
CG2 S:THR87 4.9 55.0 1.0
C S:ILE61 4.9 55.5 1.0
CG1 S:ILE70 4.9 48.8 1.0
CA S:SER84 4.9 59.9 1.0
CB S:ILE70 4.9 49.8 1.0
N S:SER84 5.0 59.6 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 04:06:57 2020

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