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Zinc in PDB 7w3e: Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K

Enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K

All present enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K:
1.9.3.1; 7.1.1.9;

Protein crystallography data

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K, PDB code: 7w3e was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.76 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.666, 203.752, 177.683, 90, 90, 90
R / Rfree (%) 16.2 / 18.2

Other elements in 7w3e:

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K (pdb code 7w3e). 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 Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K, PDB code: 7w3e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7w3e

Go back to Zinc Binding Sites List in 7w3e
Zinc binding site 1 out of 2 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:29.1
occ:1.00
SG F:CYS62 2.3 28.0 1.0
SG F:CYS85 2.3 29.0 1.0
SG F:CYS82 2.4 27.3 1.0
SG F:CYS60 2.4 27.3 1.0
CB F:CYS82 3.2 25.6 1.0
CB F:CYS62 3.2 26.3 1.0
CB F:CYS60 3.3 28.6 1.0
CB F:CYS85 3.3 27.7 1.0
CA F:CYS62 3.6 26.3 1.0
N F:CYS85 3.7 28.6 1.0
CA F:CYS85 4.1 28.0 1.0
N F:CYS62 4.2 28.2 1.0
O F:CYS60 4.4 26.0 1.0
OG1 F:THR87 4.4 39.3 0.5
CB F:SER84 4.4 29.6 1.0
CA F:CYS60 4.5 26.6 1.0
C F:CYS60 4.5 25.6 1.0
O F:HOH223 4.6 40.9 1.0
OG1 F:THR87 4.6 31.0 0.5
CA F:CYS82 4.6 27.3 1.0
C F:SER84 4.7 31.8 1.0
OG F:SER84 4.7 34.4 1.0
C F:CYS85 4.8 30.1 1.0
N F:GLY86 4.9 28.2 1.0
C F:ILE61 4.9 29.7 1.0
C F:CYS62 4.9 30.8 1.0
CB F:ILE70 5.0 25.2 1.0
CA F:SER84 5.0 27.1 1.0
CG1 F:ILE70 5.0 26.0 1.0
N F:SER84 5.0 27.6 1.0

Zinc binding site 2 out of 2 in 7w3e

Go back to Zinc Binding Sites List in 7w3e
Zinc binding site 2 out of 2 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:28.9
occ:1.00
SG S:CYS82 2.3 28.3 1.0
SG S:CYS62 2.3 28.7 1.0
SG S:CYS60 2.3 28.0 1.0
SG S:CYS85 2.3 30.0 1.0
CB S:CYS82 3.2 27.2 1.0
CB S:CYS62 3.2 28.2 1.0
CB S:CYS60 3.3 28.3 1.0
CB S:CYS85 3.4 30.4 1.0
CA S:CYS62 3.6 27.4 1.0
N S:CYS85 3.7 30.4 1.0
CA S:CYS85 4.1 30.7 1.0
OG1 S:THR87 4.1 54.0 0.6
N S:CYS62 4.2 28.8 1.0
O S:CYS60 4.4 26.2 1.0
CB S:SER84 4.4 30.6 1.0
C S:CYS60 4.5 24.9 1.0
O S:HOH227 4.5 41.7 1.0
CA S:CYS60 4.5 28.4 1.0
CA S:CYS82 4.6 26.8 1.0
C S:SER84 4.7 35.0 1.0
CG2 S:THR87 4.7 32.0 0.4
OG S:SER84 4.7 37.1 1.0
C S:CYS85 4.8 31.4 1.0
C S:ILE61 4.9 28.9 1.0
CB S:ILE70 4.9 25.7 1.0
CA S:SER84 5.0 28.9 1.0
N S:SER84 5.0 30.2 1.0
N S:GLY86 5.0 29.3 1.0
C S:CYS62 5.0 34.5 1.0

Reference:

A.Shimada, J.Baba, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K. To Be Published.
Page generated: Sat Apr 8 05:08:51 2023

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