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Chlorine in PDB 8p58: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R.:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R., PDB code: 8p58 was solved by E.Costanzi, N.Demitri, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.48 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.688, 100.828, 104.329, 90, 90, 90
R / Rfree (%) 15.9 / 17.9

Other elements in 8p58:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R. (pdb code 8p58). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R., PDB code: 8p58:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8p58

Go back to Chlorine Binding Sites List in 8p58
Chlorine binding site 1 out of 2 in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:18.1
occ:1.00
 HE21 A:GLN110 2.5 23.1 1.0
H A:GLN107 2.5 20.8 1.0
HA A:ILE106 3.1 18.0 1.0
HB2 A:GLN110 3.2 17.2 1.0
NE2 A:GLN110 3.3 19.2 1.0
HG2 A:GLN110 3.3 18.7 1.0
N A:GLN107 3.3 17.3 1.0
HG2 A:GLN107 3.4 31.4 1.0
HB A:ILE106 3.4 15.4 1.0
HB2 A:GLN107 3.4 27.7 1.0
HG22 A:ILE106 3.5 19.5 1.0
O A:HOH513 3.7 43.4 1.0
CA A:ILE106 3.8 15.0 1.0
HE22 A:GLN110 3.8 23.1 1.0
CG A:GLN110 3.9 15.6 1.0
CB A:ILE106 3.9 12.8 1.0
CB A:GLN110 3.9 14.3 1.0
CB A:GLN107 4.0 23.0 1.0
CG A:GLN107 4.0 26.2 1.0
C A:ILE106 4.1 18.6 1.0
CD A:GLN110 4.1 16.9 1.0
CG2 A:ILE106 4.1 16.2 1.0
HB3 A:GLN110 4.2 17.2 1.0
CA A:GLN107 4.2 19.1 1.0
HG3 A:GLN107 4.3 31.4 1.0
HG21 A:ILE106 4.6 19.5 1.0
O A:GLN107 4.6 16.9 1.0
HG3 A:GLN110 4.8 18.7 1.0
HG23 A:ILE106 4.9 19.5 1.0
O A:ARG105 4.9 20.4 1.0
HB3 A:GLN107 4.9 27.7 1.0
C A:GLN107 4.9 18.7 1.0
O A:HOH777 5.0 33.7 1.0

Chlorine binding site 2 out of 2 in 8p58

Go back to Chlorine Binding Sites List in 8p58
Chlorine binding site 2 out of 2 in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer R. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:49.8
occ:1.00
 H B:TYR54 2.5 33.5 1.0
HD2 B:TYR54 3.1 31.4 1.0
HA B:ASN53 3.2 43.9 1.0
HB2 B:TYR54 3.2 32.1 1.0
N B:TYR54 3.3 27.9 1.0
O B:PRO52 3.4 37.6 1.0
CD2 B:TYR54 3.9 26.1 1.0
H B:GLU55 4.0 37.4 1.0
CA B:ASN53 4.0 36.5 1.0
CB B:TYR54 4.0 26.7 1.0
C B:ASN53 4.2 29.6 1.0
HH12 B:ARG40 4.2 25.8 1.0
HH22 B:ARG40 4.2 23.7 1.0
CA B:TYR54 4.2 25.5 1.0
C B:PRO52 4.4 40.3 1.0
CG B:TYR54 4.4 26.5 1.0
NH1 B:ARG40 4.6 21.5 1.0
NH2 B:ARG40 4.7 19.8 1.0
N B:ASN53 4.7 33.6 1.0
N B:GLU55 4.7 31.1 1.0
OD1 B:ASN53 4.7 36.5 1.0
HG2 B:PRO52 4.8 42.0 1.0
HB3 B:TYR54 4.8 32.1 1.0
CE2 B:TYR54 5.0 22.2 1.0
CZ B:ARG40 5.0 19.7 1.0
HA B:TYR54 5.0 30.6 1.0

Reference:

S.Albani, E.Costanzi, G.L.Hoang, M.Kuzikov, M.Frings, N.Ansari, N.Demitri, T.T.Nguyen, V.Rizzi, J.B.Schulz, C.Bolm, A.Zaliani, P.Carloni, P.Storici, G.Rossetti. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the Sars-Cov-2 Main Protease. J.Chem.Inf.Model. V. 64 892 2024.
ISSN: ESSN 1549-960X
PubMed: 38051605
DOI: 10.1021/ACS.JCIM.3C01497
Page generated: Sun Jul 13 13:03:12 2025

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