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Sodium in PDB 7bb2: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1))

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1))

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1)):
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 the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1)), PDB code: 7bb2 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) 55.96 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.517, 100.028, 103.753, 90, 90, 90
R / Rfree (%) 16.4 / 18.9

Other elements in 7bb2:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1)) 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 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1)) (pdb code 7bb2). 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 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1)), PDB code: 7bb2:

Sodium binding site 1 out of 1 in 7bb2

Go back to Sodium Binding Sites List in 7bb2
Sodium binding site 1 out of 1 in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1))


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 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1)) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:33.9
occ:1.00
 OD2 B:ASP263 2.2 46.6 1.0
O B:PHE223 2.3 28.9 1.0
OD1 B:ASN221 2.3 29.5 1.0
O B:HOH532 2.4 28.6 1.0
O B:ASN221 2.6 29.2 1.0
HB3 B:ALA266 2.9 42.6 1.0
O B:ASP263 3.0 34.5 1.0
H B:PHE223 3.1 30.2 1.0
H B:ASN221 3.1 36.8 1.0
C B:ASN221 3.3 31.2 1.0
C B:PHE223 3.4 29.9 1.0
CG B:ASP263 3.4 52.5 1.0
N B:PHE223 3.4 25.2 1.0
CG B:ASN221 3.5 32.5 1.0
HA B:ASP263 3.5 51.7 1.0
C B:ASP263 3.8 44.4 1.0
CB B:ALA266 3.8 35.6 1.0
N B:ASN221 3.9 30.7 1.0
CA B:PHE223 3.9 26.7 1.0
HB1 B:ALA266 4.0 42.6 1.0
CA B:ASP263 4.0 43.0 1.0
C B:ARG222 4.0 25.9 1.0
CA B:ASN221 4.0 29.8 1.0
O B:HOH601 4.1 50.8 1.0
H B:SER267 4.1 40.8 1.0
HB2 B:PHE223 4.1 29.7 1.0
OD1 B:ASP263 4.2 63.4 1.0
N B:ARG222 4.2 26.6 1.0
CB B:ASP263 4.3 49.8 1.0
HB2 B:ALA266 4.3 42.6 1.0
OG B:SER267 4.3 32.6 1.0
HA B:THR224 4.3 39.2 1.0
HD21 B:ASN221 4.3 41.5 1.0
CB B:ASN221 4.3 31.0 1.0
ND2 B:ASN221 4.4 34.6 1.0
HG B:SER267 4.5 39.1 1.0
N B:THR224 4.5 26.6 1.0
N B:SER267 4.5 34.0 1.0
CA B:ARG222 4.5 27.5 1.0
HA B:ARG222 4.5 33.0 1.0
CB B:PHE223 4.6 24.8 1.0
O B:ARG222 4.7 26.9 1.0
HG23 B:ILE259 4.7 57.1 1.0
HB3 B:ASP263 4.8 59.8 1.0
HA B:PHE223 4.8 32.0 1.0
HB2 B:ASN221 4.8 37.2 1.0
H B:ALA266 4.8 44.3 1.0
HA B:LEU220 4.8 36.8 1.0
O B:HOH583 4.8 50.6 1.0
CA B:ALA266 4.9 36.1 1.0
C B:ALA266 4.9 37.3 1.0
N B:MET264 4.9 37.8 1.0
H B:ARG222 4.9 31.9 1.0
HA B:MET264 4.9 44.8 1.0
CA B:THR224 4.9 32.7 1.0
HA B:ASN221 4.9 35.7 1.0
HB2 B:ASP263 5.0 59.8 1.0

Reference:

E.Costanzi, N.Demitri, B.Giabbai, P.Storici. Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 at 1.6A Resolution (Spacegroup P2(1)2(1)2(1)) To Be Published.
Page generated: Tue Oct 8 16:08:34 2024

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