Zinc in PDB 8ijn: Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K

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

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 8ijn was solved by T.Tsukihara, A.Shimada, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.37 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.289, 208.358, 177.916, 90, 90, 90
R / Rfree (%) 16.9 / 19.2

Other elements in 8ijn:

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K (pdb code 8ijn). 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 Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 8ijn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8ijn

Go back to Zinc Binding Sites List in 8ijn
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:29.8
occ:1.00
SG F:CYS85 2.3 32.5 1.0
SG F:CYS60 2.3 31.8 1.0
SG F:CYS62 2.3 31.2 1.0
SG F:CYS82 2.3 32.2 1.0
CB F:CYS82 3.2 27.8 1.0
CB F:CYS85 3.3 32.9 1.0
CB F:CYS60 3.3 33.5 1.0
CB F:CYS62 3.3 32.4 1.0
CA F:CYS62 3.6 32.3 1.0
N F:CYS85 3.7 31.6 1.0
CA F:CYS85 4.1 34.3 1.0
N F:CYS62 4.2 31.6 1.0
O F:CYS60 4.4 28.1 1.0
C F:CYS60 4.5 32.8 1.0
CB F:SER84 4.5 31.1 1.0
CA F:CYS60 4.5 31.0 1.0
O F:HOH205 4.6 43.4 1.0
OG1 F:THR87 4.6 54.6 1.0
CA F:CYS82 4.6 25.7 1.0
OG F:SER84 4.6 39.0 1.0
C F:SER84 4.7 37.5 1.0
C F:CYS85 4.8 34.4 1.0
C F:ILE61 4.9 37.2 1.0
CB F:ILE70 4.9 29.4 1.0
C F:CYS62 4.9 42.3 1.0
CA F:SER84 5.0 30.1 1.0
CG2 F:THR87 5.0 43.4 1.0
N F:GLY86 5.0 33.0 1.0
N F:SER84 5.0 32.6 1.0
CG1 F:ILE70 5.0 29.0 1.0

Zinc binding site 2 out of 2 in 8ijn

Go back to Zinc Binding Sites List in 8ijn
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:31.4
occ:1.00
SG S:CYS60 2.3 32.8 1.0
SG S:CYS85 2.3 34.6 1.0
SG S:CYS82 2.3 32.5 1.0
SG S:CYS62 2.3 35.0 1.0
CB S:CYS82 3.2 28.0 1.0
CB S:CYS60 3.3 32.8 1.0
CB S:CYS62 3.3 30.3 1.0
CB S:CYS85 3.3 32.7 1.0
CA S:CYS62 3.6 31.0 1.0
N S:CYS85 3.7 31.3 1.0
CA S:CYS85 4.1 31.9 1.0
N S:CYS62 4.2 32.9 1.0
O S:CYS60 4.4 30.1 1.0
OG1 S:THR87 4.4 44.7 1.0
C S:CYS60 4.4 36.2 1.0
CA S:CYS60 4.5 32.4 1.0
CB S:SER84 4.5 34.6 1.0
O S:HOH207 4.6 42.7 1.0
CA S:CYS82 4.6 33.0 1.0
OG S:SER84 4.7 38.5 1.0
C S:SER84 4.7 43.9 1.0
C S:CYS85 4.8 37.6 1.0
C S:ILE61 4.9 34.3 1.0
N S:GLY86 4.9 33.2 1.0
CG1 S:ILE70 4.9 27.4 1.0
C S:CYS62 5.0 46.2 1.0
CA S:SER84 5.0 35.9 1.0
CB S:ILE70 5.0 27.3 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: ESSN 1091-6490
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Wed Apr 26 00:48:04 2023

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