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Sodium in PDB 7bgp: Crystal Structure of Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt.

Enzymatic activity of Crystal Structure of Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt.

All present enzymatic activity of Crystal Structure of Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt.:
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 Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt., PDB code: 7bgp 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) 45.94 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.853, 99.779, 103.514, 90, 90, 90
R / Rfree (%) 17 / 20.1

Other elements in 7bgp:

The structure of Crystal Structure of Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt. (pdb code 7bgp). 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 Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt., PDB code: 7bgp:

Sodium binding site 1 out of 1 in 7bgp

Go back to Sodium Binding Sites List in 7bgp
Sodium binding site 1 out of 1 in the Crystal Structure of Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt.


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 Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:44.2
occ:1.00
 OD1 B:ASN221 2.2 34.8 1.0
OD1 B:ASP263 2.2 50.9 1.0
O B:PHE223 2.3 29.1 1.0
O B:HOH510 2.5 32.0 1.0
O B:ASN221 2.7 29.9 1.0
H B:PHE223 2.9 34.6 1.0
O B:ASP263 3.0 35.4 1.0
HB3 B:ALA266 3.1 44.4 1.0
H B:ASN221 3.3 41.0 1.0
N B:PHE223 3.3 28.9 1.0
CG B:ASN221 3.3 33.5 1.0
C B:ASN221 3.3 31.6 1.0
C B:PHE223 3.3 30.6 1.0
CG B:ASP263 3.4 54.0 1.0
HA B:ASP263 3.5 51.2 1.0
C B:ASP263 3.8 36.4 1.0
CA B:PHE223 3.8 32.1 1.0
C B:ARG222 3.9 29.6 1.0
N B:ASN221 3.9 34.2 1.0
CB B:ALA266 4.0 37.1 1.0
HB2 B:PHE223 4.0 36.7 1.0
CA B:ASP263 4.0 42.6 1.0
CA B:ASN221 4.0 30.1 1.0
HB1 B:ALA266 4.0 44.4 1.0
HG B:SER267 4.1 45.7 1.0
N B:ARG222 4.1 28.9 1.0
HD21 B:ASN221 4.1 39.8 1.0
H B:SER267 4.1 47.1 1.0
ND2 B:ASN221 4.2 33.2 1.0
OG B:SER267 4.2 38.1 1.0
CB B:ASN221 4.3 26.6 1.0
CB B:ASP263 4.3 42.1 1.0
OD2 B:ASP263 4.3 54.2 1.0
HA B:THR224 4.4 51.4 1.0
CA B:ARG222 4.4 29.1 1.0
CB B:PHE223 4.5 30.5 1.0
N B:SER267 4.5 39.2 1.0
HB2 B:ALA266 4.5 44.4 1.0
HA B:ARG222 4.5 34.9 1.0
N B:THR224 4.5 32.2 1.0
O B:ARG222 4.6 30.7 1.0
HA B:PHE223 4.7 38.6 1.0
H B:ARG222 4.7 34.7 1.0
HB2 B:ASN221 4.8 31.9 1.0
C B:ALA266 4.8 37.9 1.0
HB3 B:ASP263 4.9 50.6 1.0
H B:ALA266 4.9 45.8 1.0
CA B:ALA266 4.9 36.2 1.0
HA B:MET264 4.9 40.9 1.0
N B:MET264 4.9 32.6 1.0
HA B:ASN221 4.9 36.1 1.0
HB2 B:ASP263 5.0 50.6 1.0
HB3 B:ASN221 5.0 31.9 1.0
HD22 B:ASN221 5.0 39.8 1.0
HA B:LEU220 5.0 39.9 1.0

Reference:

E.Costanzi, N.Demitri, B.Giabbai, P.Storici. Crystal Structure of Mg-132 Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Absence of Dtt. To Be Published.
Page generated: Tue Oct 8 16:12:38 2024

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