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Sodium in PDB 8p56: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77.:
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 150 Micromolar X77., PDB code: 8p56 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) 45.45 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.941, 101.009, 104.201, 90, 90, 90
R / Rfree (%) 16.3 / 18.4

Other elements in 8p56:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 150 Micromolar X77. 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 150 Micromolar X77. (pdb code 8p56). 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 150 Micromolar X77., PDB code: 8p56:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8p56

Go back to Sodium Binding Sites List in 8p56
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 150 Micromolar X77.


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 150 Micromolar X77. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:31.5
occ:1.00
 OD1 B:ASP263 2.2 47.3 1.0
O B:PHE223 2.3 23.8 1.0
OD1 B:ASN221 2.3 27.1 1.0
O B:HOH624 2.4 25.9 1.0
O B:ASN221 2.5 26.3 1.0
HB3 B:ALA266 3.0 39.3 1.0
H B:PHE223 3.1 27.7 1.0
H B:ASN221 3.1 35.9 1.0
O B:ASP263 3.2 31.5 1.0
C B:ASN221 3.3 26.5 1.0
C B:PHE223 3.4 23.6 1.0
CG B:ASN221 3.4 28.6 1.0
CG B:ASP263 3.4 48.1 1.0
N B:PHE223 3.4 23.1 1.0
HA B:ASP263 3.6 42.9 1.0
N B:ASN221 3.9 29.9 1.0
CB B:ALA266 3.9 32.8 1.0
CA B:PHE223 3.9 23.5 1.0
C B:ASP263 3.9 36.0 1.0
HB1 B:ALA266 4.0 39.3 1.0
CA B:ASN221 4.0 27.9 1.0
C B:ARG222 4.0 22.8 1.0
HB2 B:PHE223 4.1 27.3 1.0
CA B:ASP263 4.1 35.8 1.0
N B:ARG222 4.2 23.1 1.0
OD2 B:ASP263 4.2 53.6 1.0
HD21 B:ASN221 4.2 35.6 1.0
H B:SER267 4.2 34.8 1.0
O B:HOH726 4.3 51.3 1.0
CB B:ASN221 4.3 28.2 1.0
ND2 B:ASN221 4.3 29.7 1.0
HA B:THR224 4.3 34.7 1.0
OG B:SER267 4.3 32.3 1.0
HB2 B:ALA266 4.3 39.3 1.0
CB B:ASP263 4.4 45.7 1.0
CA B:ARG222 4.5 24.9 1.0
N B:THR224 4.5 23.9 1.0
HA B:ARG222 4.5 29.9 1.0
N B:SER267 4.6 28.9 1.0
CB B:PHE223 4.6 22.8 1.0
HG22 B:THR224 4.6 45.9 1.0
HG B:SER267 4.6 38.7 1.0
O B:ARG222 4.7 24.5 1.0
HA B:PHE223 4.7 28.3 1.0
HB2 B:ASN221 4.7 33.8 1.0
O B:HOH791 4.7 49.9 1.0
H B:ARG222 4.8 27.7 1.0
HG23 B:THR224 4.9 45.9 1.0
C B:ALA266 4.9 30.7 1.0
HA B:LEU220 4.9 33.4 1.0
H B:ALA266 4.9 34.8 1.0
CA B:ALA266 4.9 30.4 1.0
HA B:ASN221 4.9 33.5 1.0
CA B:THR224 4.9 28.9 1.0
HB2 B:ASP263 4.9 54.9 1.0
HG23 B:ILE259 5.0 60.0 1.0
HB3 B:ASP263 5.0 54.9 1.0
HB3 B:ASN221 5.0 33.8 1.0

Sodium binding site 2 out of 2 in 8p56

Go back to Sodium Binding Sites List in 8p56
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 150 Micromolar X77.


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 150 Micromolar X77. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:42.2
occ:1.00
 HH B:TYR101 1.8 33.4 1.0
OD2 B:ASP33 2.2 42.0 1.0
HB2 B:ASP33 2.4 34.3 1.0
O B:HOH652 2.5 32.1 1.0
OH B:TYR101 2.5 27.8 1.0
CG B:ASP33 3.0 45.0 1.0
CB B:ASP33 3.1 28.6 1.0
HE1 B:TYR101 3.1 28.8 1.0
CZ B:TYR101 3.5 23.1 1.0
HB3 B:ASP33 3.6 34.3 1.0
CE1 B:TYR101 3.7 24.0 1.0
HB3 B:LEU32 3.8 25.5 1.0
O B:LEU32 3.9 22.9 1.0
C B:LEU32 4.1 22.5 1.0
O B:HOH611 4.1 39.5 1.0
OD1 B:ASP33 4.1 45.6 1.0
HB2 B:LEU32 4.2 25.5 1.0
N B:ASP33 4.2 23.8 1.0
CA B:ASP33 4.3 25.9 1.0
CB B:LEU32 4.4 21.2 1.0
HG21 B:THR98 4.4 31.2 1.0
H B:ASP33 4.6 28.6 1.0
CE2 B:TYR101 4.8 22.4 1.0
H B:ASP34 4.9 37.2 1.0
OH B:TYR37 4.9 26.4 1.0
HA B:ASP33 4.9 31.1 1.0
CA B:LEU32 4.9 22.4 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 14:58:41 2025

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