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Sodium in PDB 7b3e: Crystal Structure of Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2

Enzymatic activity of Crystal Structure of Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2

All present enzymatic activity of Crystal Structure of Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2, PDB code: 7b3e was solved by E.Costanzi, N.Demitri, B.Giabbai, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.48 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.834, 101.104, 103.559, 90, 90, 90
R / Rfree (%) 17.1 / 20.4

Other elements in 7b3e:

The structure of Crystal Structure of Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 (pdb code 7b3e). 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 Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2, PDB code: 7b3e:

Sodium binding site 1 out of 1 in 7b3e

Go back to Sodium Binding Sites List in 7b3e
Sodium binding site 1 out of 1 in the Crystal Structure of Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2


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 Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:40.9
occ:1.00
 OD2 B:ASP263 2.1 51.1 1.0
O B:PHE223 2.3 36.0 1.0
OD1 B:ASN221 2.3 39.8 1.0
O B:HOH722 2.4 31.9 1.0
O B:ASN221 2.6 32.6 1.0
HB3 B:ALA266 3.0 53.4 1.0
O B:ASP263 3.0 42.9 1.0
H B:PHE223 3.1 42.5 1.0
H B:ASN221 3.2 45.4 1.0
HA B:ASP263 3.3 57.8 1.0
CG B:ASP263 3.3 60.8 1.0
C B:ASN221 3.4 32.4 1.0
C B:PHE223 3.4 37.2 1.0
N B:PHE223 3.4 35.5 1.0
CG B:ASN221 3.4 39.8 1.0
C B:ASP263 3.6 43.7 1.0
CA B:ASP263 3.8 48.1 1.0
CB B:ALA266 3.9 44.5 1.0
N B:ASN221 3.9 37.8 1.0
CA B:PHE223 3.9 36.8 1.0
C B:ARG222 4.1 35.5 1.0
CA B:ASN221 4.1 38.1 1.0
HB1 B:ALA266 4.1 53.4 1.0
CB B:ASP263 4.1 47.9 1.0
HB2 B:PHE223 4.1 44.2 1.0
H B:SER267 4.2 46.6 1.0
N B:ARG222 4.2 33.1 1.0
OD1 B:ASP263 4.2 61.3 1.0
HD21 B:ASN221 4.3 52.4 1.0
ND2 B:ASN221 4.3 43.6 1.0
HB2 B:ALA266 4.3 53.4 1.0
CB B:ASN221 4.3 35.7 1.0
HA B:THR224 4.3 47.9 1.0
OG B:SER267 4.4 43.2 1.0
HG B:SER267 4.4 51.8 1.0
N B:THR224 4.5 38.5 1.0
CA B:ARG222 4.5 34.5 1.0
HA B:ARG222 4.6 41.4 1.0
N B:SER267 4.6 38.9 1.0
CB B:PHE223 4.6 36.9 1.0
HB3 B:ASP263 4.7 57.5 1.0
HG23 B:ILE259 4.7 65.0 1.0
HB2 B:ASP263 4.7 57.5 1.0
N B:MET264 4.8 43.5 1.0
HA B:PHE223 4.8 44.1 1.0
O B:ARG222 4.8 36.6 1.0
H B:ALA266 4.8 49.0 1.0
HB2 B:ASN221 4.8 42.8 1.0
HA B:LEU220 4.9 44.2 1.0
H B:ARG222 4.9 39.7 1.0
CA B:ALA266 4.9 48.0 1.0
CA B:THR224 4.9 39.9 1.0
HA B:MET264 4.9 52.9 1.0
C B:ALA266 5.0 43.1 1.0
HA B:ASN221 5.0 45.7 1.0

Reference:

E.Costanzi, N.Demitri, B.Giabbai, P.Storici. Crystal Structure of Myricetin Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 To Be Published.
Page generated: Mon Aug 18 09:13:58 2025

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