Zinc in PDB 8dpr: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248, PDB code: 8dpr was solved by H.Bulut, H.Hayashi, K.Tsuji, N.Kuwata, D.Das, H.Tamamura, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.52 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.403, 53.926, 45.678, 90, 101.63, 90
R / Rfree (%) 19 / 24.7

Other elements in 8dpr:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 (pdb code 8dpr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248, PDB code: 8dpr:

Zinc binding site 1 out of 1 in 8dpr

Go back to Zinc Binding Sites List in 8dpr
Zinc binding site 1 out of 1 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:51.0
occ:0.50
 O A:ASN203 2.7 25.6 1.0
O A:GLU288 2.8 30.8 1.0
N A:PHE291 2.9 31.2 1.0
O A:PHE291 3.1 27.1 1.0
CA A:ASP289 3.2 30.4 1.0
N A:GLU290 3.2 29.6 1.0
C A:ASN203 3.3 28.4 1.0
C A:ASP289 3.3 31.0 1.0
C A:GLU288 3.3 32.4 1.0
N A:ASP289 3.5 29.0 1.0
CB A:ASN203 3.5 28.7 1.0
CB A:TRP207 3.6 33.8 1.0
CA A:PHE291 3.6 30.3 1.0
CB A:PHE291 3.6 33.0 1.0
C A:PHE291 3.8 28.5 1.0
CA A:ASN203 3.9 28.1 1.0
CD2 A:PHE291 3.9 34.3 1.0
N A:VAL204 3.9 28.4 1.0
C A:GLU290 4.0 34.8 1.0
O A:ASP289 4.0 35.2 1.0
CA A:GLU290 4.2 32.5 1.0
CB A:GLU288 4.2 40.4 1.0
CG A:PHE291 4.3 35.9 1.0
CA A:VAL204 4.3 31.2 1.0
CG A:TRP207 4.3 37.5 1.0
N A:TRP207 4.5 28.5 1.0
CA A:GLU288 4.5 33.1 1.0
CA A:TRP207 4.6 32.5 1.0
CB A:ASP289 4.6 30.5 1.0
CG A:ASN203 4.7 29.2 1.0
CD1 A:TRP207 4.8 38.2 1.0
C A:VAL204 5.0 32.3 1.0

Reference:

H.Bulut, H.Hayashi, K.Tsuji, N.Higashi-Kuwata, D.Das, H.Tamamura, H.Mitsuya. A Small Molecule Compound Inhibits the Main Protease of Sars-Cov-2 and Blocks Virus Replication. To Be Published.
Page generated: Wed Oct 30 19:14:49 2024

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