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Sodium in PDB 8ri4: Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2- Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2,3-F]Benzimidazol-3-Yl)-(P- Tolyl)Methanone

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2- Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2,3-F]Benzimidazol-3-Yl)-(P- Tolyl)Methanone

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2- Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2,3-F]Benzimidazol-3-Yl)-(P- Tolyl)Methanone:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2- Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2,3-F]Benzimidazol-3-Yl)-(P- Tolyl)Methanone, PDB code: 8ri4 was solved by J.Charton, B.Deprez, X.Hanoulle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.46 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.247, 54.004, 44.68, 90, 101.14, 90
R / Rfree (%) 18.9 / 23.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2- Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2,3-F]Benzimidazol-3-Yl)-(P- Tolyl)Methanone (pdb code 8ri4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2- Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2,3-F]Benzimidazol-3-Yl)-(P- Tolyl)Methanone, PDB code: 8ri4:

Sodium binding site 1 out of 1 in 8ri4

Go back to Sodium Binding Sites List in 8ri4
Sodium binding site 1 out of 1 in the Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2- Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2,3-F]Benzimidazol-3-Yl)-(P- Tolyl)Methanone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2- Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2,3-F]Benzimidazol-3-Yl)-(P- Tolyl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:19.2
occ:1.00
 H A:PHE291 2.0 14.0 1.0
HB2 A:TRP207 2.7 12.6 1.0
HA A:ASP289 2.7 14.7 1.0
O A:GLU288 2.7 14.1 1.0
O A:ASN203 2.7 9.5 1.0
HB3 A:ASN203 2.7 9.6 1.0
HD2 A:PHE291 2.8 21.2 1.0
HB2 A:PHE291 2.8 15.9 1.0
N A:PHE291 2.9 12.6 1.0
O A:PHE291 3.1 12.5 1.0
C A:ASP289 3.3 14.2 1.0
CA A:ASP289 3.3 15.2 1.0
C A:ASN203 3.3 9.2 1.0
H A:GLU290 3.3 15.0 1.0
HB3 A:TRP207 3.3 12.6 1.0
N A:GLU290 3.3 14.6 1.0
C A:GLU288 3.4 14.4 1.0
CB A:TRP207 3.4 13.3 1.0
CB A:PHE291 3.5 15.3 1.0
CA A:PHE291 3.5 14.1 1.0
HA A:VAL204 3.5 9.5 1.0
CB A:ASN203 3.6 9.5 1.0
CD2 A:PHE291 3.6 20.2 1.0
N A:ASP289 3.7 13.6 1.0
C A:PHE291 3.7 12.8 1.0
H A:TRP207 3.9 11.0 1.0
C A:GLU290 3.9 17.2 1.0
N A:VAL204 3.9 9.3 1.0
O A:ASP289 3.9 14.1 1.0
CA A:ASN203 4.0 9.3 1.0
HB2 A:ASN203 4.0 9.6 1.0
CG A:PHE291 4.0 19.6 1.0
HB3 A:GLU288 4.1 19.2 1.0
HB2 A:GLU288 4.1 19.2 1.0
HA A:ASN203 4.1 9.4 1.0
CA A:GLU290 4.2 16.6 1.0
CG A:TRP207 4.2 12.3 1.0
CA A:VAL204 4.2 9.5 1.0
HB3 A:PHE291 4.3 15.9 1.0
H A:ASP289 4.4 14.1 1.0
N A:TRP207 4.4 10.6 1.0
CB A:GLU288 4.5 18.1 1.0
HA A:PHE291 4.5 13.8 1.0
CA A:TRP207 4.5 11.5 1.0
H A:VAL204 4.5 9.3 1.0
CA A:GLU288 4.6 17.1 1.0
HB2 A:ALA206 4.6 11.2 1.0
HD21 A:ASN203 4.6 10.0 1.0
CB A:ASP289 4.6 15.1 1.0
CD1 A:TRP207 4.7 13.6 1.0
HA A:GLU290 4.7 16.7 1.0
HD1 A:TRP207 4.7 13.4 1.0
HB2 A:ASP289 4.7 15.4 1.0
CG A:ASN203 4.7 10.0 1.0
HA A:TRP207 4.8 11.7 1.0
CE2 A:PHE291 4.8 25.8 1.0
O A:HOH507 4.8 22.3 1.0
HG23 A:VAL204 4.8 9.3 1.0
HE2 A:PHE291 4.9 24.4 1.0
CD2 A:TRP207 5.0 12.3 1.0
ND2 A:ASN203 5.0 10.1 1.0
C A:VAL204 5.0 9.4 1.0

Reference:

J.Charton, X.Hanoulle, B.Deprez. Crystal Structure of the Sars-Cov-2 Main Protease Inhibited By (2-Methylsulfanyl-6,7-Dihydro-[1,4]Dioxino[2, 3-F]Benzimidazol-3-Yl)-(P-Tolyl)Methanone To Be Published.
Page generated: Sat Feb 8 23:42:13 2025

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