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Sodium 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:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8p58

Go back to Sodium Binding Sites List in 8p58
Sodium 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 Sodium with other atoms in the Na 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
B:Na405

b:30.4
occ:1.00
 OD1 B:ASP263 2.1 42.5 1.0
O B:PHE223 2.3 23.1 1.0
OD1 B:ASN221 2.4 25.0 1.0
O B:ASN221 2.5 26.8 1.0
O B:HOH522 2.5 26.0 1.0
HB3 B:ALA266 3.0 34.6 1.0
H B:PHE223 3.1 27.8 1.0
H B:ASN221 3.2 29.7 1.0
O B:ASP263 3.2 28.7 1.0
C B:ASN221 3.3 22.6 1.0
C B:PHE223 3.4 23.5 1.0
CG B:ASP263 3.4 42.8 1.0
N B:PHE223 3.4 23.2 1.0
CG B:ASN221 3.5 27.6 1.0
HA B:ASP263 3.6 39.5 1.0
N B:ASN221 3.9 24.7 1.0
C B:ASP263 3.9 33.4 1.0
CB B:ALA266 3.9 28.9 1.0
CA B:PHE223 3.9 23.9 1.0
C B:ARG222 4.0 23.9 1.0
CA B:ASN221 4.0 25.0 1.0
HB1 B:ALA266 4.1 34.6 1.0
CA B:ASP263 4.1 32.9 1.0
N B:ARG222 4.1 22.7 1.0
HB2 B:PHE223 4.1 28.6 1.0
OD2 B:ASP263 4.2 49.3 1.0
HA B:THR224 4.2 33.3 1.0
HD21 B:ASN221 4.3 29.5 1.0
CB B:ASP263 4.3 37.5 1.0
H B:SER267 4.3 30.8 1.0
CB B:ASN221 4.3 22.2 1.0
ND2 B:ASN221 4.4 24.6 1.0
HB2 B:ALA266 4.4 34.6 1.0
HG22 B:THR224 4.4 47.2 1.0
CA B:ARG222 4.4 23.7 1.0
HA B:ARG222 4.5 28.3 1.0
OG B:SER267 4.5 27.0 1.0
N B:THR224 4.5 24.5 1.0
O B:ARG222 4.6 24.8 1.0
CB B:PHE223 4.6 23.8 1.0
N B:SER267 4.7 25.6 1.0
HA B:PHE223 4.7 28.7 1.0
HG23 B:THR224 4.7 47.2 1.0
H B:ARG222 4.8 27.1 1.0
HG B:SER267 4.8 32.4 1.0
HB2 B:ASN221 4.8 26.7 1.0
CA B:THR224 4.9 27.7 1.0
HB3 B:ASP263 4.9 45.0 1.0
HG23 B:ILE259 4.9 43.5 0.5
HA B:ASN221 4.9 30.0 1.0
HA B:LEU220 4.9 26.3 1.0
H B:ALA266 4.9 32.5 1.0
HB2 B:ASP263 5.0 45.0 1.0
CA B:ALA266 5.0 26.8 1.0
C B:ALA266 5.0 29.2 1.0

Sodium binding site 2 out of 2 in 8p58

Go back to Sodium Binding Sites List in 8p58
Sodium 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 Sodium with other atoms in the Na 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:Na406

b:34.2
occ:1.00
 HH B:TYR101 1.8 27.8 1.0
OD2 B:ASP33 2.3 40.8 1.0
OH B:TYR101 2.6 23.1 1.0
HB2 B:ASP33 2.6 30.8 1.0
O B:HOH545 2.7 23.1 1.0
HE1 B:TYR101 3.1 26.6 1.0
CG B:ASP33 3.1 30.6 1.0
CB B:ASP33 3.3 25.6 1.0
CZ B:TYR101 3.5 20.9 1.0
CE1 B:TYR101 3.6 22.1 1.0
HB3 B:ASP33 3.8 30.8 1.0
HB3 B:LEU32 3.8 22.9 1.0
O B:LEU32 4.1 20.1 1.0
HB2 B:LEU32 4.2 22.9 1.0
O B:HOH530 4.2 39.3 1.0
C B:LEU32 4.2 20.0 1.0
OD1 B:ASP33 4.3 38.9 1.0
N B:ASP33 4.3 24.2 1.0
CB B:LEU32 4.4 19.1 1.0
CA B:ASP33 4.4 25.0 1.0
HG21 B:THR98 4.5 28.3 1.0
H B:ASP33 4.7 29.1 1.0
OH B:TYR37 4.8 23.6 1.0
CE2 B:TYR101 4.8 19.5 1.0
CD1 B:TYR101 5.0 19.3 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: Mon Aug 18 14:58:50 2025

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