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Sodium in PDB 8p5b: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer S.

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

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 S.:
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 S., PDB code: 8p5b 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) 51.86 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.93, 99.831, 103.72, 90, 90, 90
R / Rfree (%) 16.4 / 17.8

Other elements in 8p5b:

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

Chlorine (Cl) 1 atom

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 S. (pdb code 8p5b). 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 Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer S., PDB code: 8p5b:

Sodium binding site 1 out of 1 in 8p5b

Go back to Sodium Binding Sites List in 8p5b
Sodium binding site 1 out of 1 in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 500 Micromolar X77 Enantiomer S.


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 S. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:29.0
occ:1.00
 OD1 B:ASP263 2.1 39.2 1.0
O B:PHE223 2.3 23.6 1.0
OD1 B:ASN221 2.3 25.0 1.0
O B:HOH557 2.3 22.7 1.0
O B:ASN221 2.7 24.8 1.0
O B:ASP263 2.9 24.6 1.0
HB3 B:ALA266 3.0 30.8 1.0
H B:PHE223 3.0 28.1 1.0
H B:ASN221 3.2 31.3 1.0
CG B:ASP263 3.3 36.1 1.0
C B:PHE223 3.3 23.5 1.0
HA B:ASP263 3.4 31.4 1.0
CG B:ASN221 3.4 25.7 1.0
C B:ASN221 3.4 21.5 1.0
N B:PHE223 3.4 23.5 1.0
C B:ASP263 3.6 22.7 1.0
CB B:ALA266 3.9 25.6 1.0
CA B:ASP263 3.9 26.2 1.0
N B:ASN221 3.9 26.1 1.0
CA B:PHE223 3.9 24.1 1.0
HB1 B:ALA266 4.0 30.8 1.0
CA B:ASN221 4.0 21.0 1.0
HB2 B:PHE223 4.1 28.8 1.0
H B:SER267 4.1 27.4 1.0
C B:ARG222 4.1 24.2 1.0
OG B:SER267 4.2 24.6 1.0
CB B:ASP263 4.2 28.7 1.0
HD21 B:ASN221 4.2 32.3 1.0
N B:ARG222 4.2 22.7 1.0
ND2 B:ASN221 4.2 26.9 1.0
OD2 B:ASP263 4.2 51.7 1.0
CB B:ASN221 4.3 24.1 1.0
HG B:SER267 4.3 29.5 1.0
HA B:THR224 4.3 28.9 1.0
HB2 B:ALA266 4.3 30.8 1.0
N B:SER267 4.4 22.8 1.0
N B:THR224 4.5 24.5 1.0
CB B:PHE223 4.6 24.1 1.0
CA B:ARG222 4.6 23.8 1.0
HA B:ARG222 4.6 28.5 1.0
HB2 B:ASP263 4.7 34.5 1.0
HA B:PHE223 4.7 28.9 1.0
HB2 B:ASN221 4.8 28.9 1.0
N B:MET264 4.8 23.0 1.0
H B:ALA266 4.8 28.4 1.0
HA B:MET264 4.8 24.6 1.0
O B:ARG222 4.8 25.3 1.0
C B:ALA266 4.8 24.8 1.0
CA B:ALA266 4.8 27.1 1.0
HB3 B:ASP263 4.8 34.5 1.0
HA B:LEU220 4.9 26.0 1.0
H B:ARG222 4.9 27.1 1.0
HG23 B:ILE259 4.9 37.3 1.0
CA B:THR224 4.9 24.1 1.0
HA B:ASN221 4.9 25.2 1.0
O B:HOH668 5.0 48.9 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 14:59:15 2025

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