Sodium in PDB 8r11: Structure of Compound 7 Bound to Sars-Cov-2 Main Protease

Enzymatic activity of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease

All present enzymatic activity of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease:
3.4.22.69;

Protein crystallography data

The structure of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease, PDB code: 8r11 was solved by A.Mac Sweeney, J.Hazemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.02 / 1.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.088, 102.043, 104.658, 90, 90, 90
R / Rfree (%) 16.8 / 19.3

Other elements in 8r11:

The structure of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Bromine (Br) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease (pdb code 8r11). 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 Structure of Compound 7 Bound to Sars-Cov-2 Main Protease, PDB code: 8r11:

Sodium binding site 1 out of 1 in 8r11

Go back to Sodium Binding Sites List in 8r11
Sodium binding site 1 out of 1 in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na703

b:20.1
occ:1.00
OD1 B:ASP263 2.2 24.7 1.0
O B:PHE223 2.3 14.9 1.0
OD1 B:ASN221 2.3 16.8 1.0
O B:HOH885 2.4 19.2 1.0
O B:ASN221 2.6 17.4 1.0
O B:ASP263 3.1 17.8 1.0
C B:ASN221 3.3 15.3 1.0
C B:PHE223 3.4 14.3 1.0
CG B:ASN221 3.4 17.1 1.0
CG B:ASP263 3.4 20.7 1.0
N B:PHE223 3.5 14.4 1.0
N B:ASN221 3.8 17.1 1.0
C B:ASP263 3.9 17.8 1.0
CB B:ALA266 3.9 18.6 1.0
CA B:PHE223 3.9 14.3 1.0
CA B:ASN221 4.0 16.6 1.0
CA B:ASP263 4.0 17.8 1.0
C B:ARG222 4.0 15.2 1.0
N B:ARG222 4.2 15.3 1.0
O B:HOH925 4.3 39.3 1.0
CB B:ASN221 4.3 17.2 1.0
CB B:ASP263 4.3 19.7 1.0
OD2 B:ASP263 4.3 22.0 1.0
ND2 B:ASN221 4.4 17.7 1.0
OG B:SER267 4.4 18.5 1.0
CA B:ARG222 4.5 15.6 1.0
N B:THR224 4.5 14.7 1.0
CB B:PHE223 4.6 14.9 1.0
N B:SER267 4.7 16.5 1.0
O B:ARG222 4.8 15.8 1.0
CA B:THR224 4.9 16.6 1.0
CA B:ALA266 4.9 16.9 1.0
C B:ALA266 5.0 17.0 1.0

Reference:

A.Mac Sweeney, J.Hazemann. Identification of Sars-Cov-2 Mpro Inhibitors Through Deep Reinforcement Learning For De Novo Drug Design and Computational Chemistry Approaches To Be Published.
Page generated: Wed Oct 9 13:17:29 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy