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Sodium in PDB 8p57: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 75 Micromolar X77.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 75 Micromolar X77.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 75 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 75 Micromolar X77., PDB code: 8p57 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) 49.50 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.66, 100.829, 104.647, 90, 90, 90
R / Rfree (%) 16.8 / 18.3

Other elements in 8p57:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 75 Micromolar X77. 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 75 Micromolar X77. (pdb code 8p57). 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 75 Micromolar X77., PDB code: 8p57:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8p57

Go back to Sodium Binding Sites List in 8p57
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 75 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 75 Micromolar X77. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:31.3
occ:1.00
OD1 B:ASP263 2.1 42.1 1.0
O B:PHE223 2.3 24.6 1.0
O B:HOH616 2.3 26.4 1.0
OD1 B:ASN221 2.4 25.9 1.0
O B:ASN221 2.6 25.6 1.0
H B:PHE223 3.0 26.2 1.0
HB3 B:ALA266 3.0 37.5 1.0
O B:ASP263 3.1 31.9 1.0
H B:ASN221 3.2 33.0 1.0
C B:PHE223 3.3 24.5 1.0
N B:PHE223 3.3 21.8 1.0
CG B:ASP263 3.4 43.5 1.0
C B:ASN221 3.4 25.8 1.0
HA B:ASP263 3.5 43.2 1.0
CG B:ASN221 3.5 30.4 1.0
C B:ASP263 3.8 32.4 1.0
CB B:ALA266 3.9 31.3 1.0
CA B:PHE223 3.9 22.2 1.0
N B:ASN221 3.9 27.4 1.0
O B:HOH704 3.9 45.1 1.0
HB1 B:ALA266 3.9 37.5 1.0
C B:ARG222 4.0 21.7 1.0
CA B:ASP263 4.0 36.0 1.0
CA B:ASN221 4.1 26.7 1.0
HB2 B:PHE223 4.1 29.4 1.0
N B:ARG222 4.2 21.9 1.0
OD2 B:ASP263 4.2 47.5 1.0
H B:SER267 4.2 34.3 1.0
CB B:ASP263 4.3 43.4 1.0
HD21 B:ASN221 4.3 34.6 1.0
HB2 B:ALA266 4.3 37.5 1.0
HA B:THR224 4.3 32.1 1.0
OG B:SER267 4.3 29.3 1.0
ND2 B:ASN221 4.4 28.9 1.0
CB B:ASN221 4.4 27.5 1.0
CA B:ARG222 4.5 21.1 1.0
HA B:ARG222 4.5 25.2 1.0
N B:THR224 4.5 22.5 1.0
HG B:SER267 4.5 35.1 1.0
N B:SER267 4.6 28.6 1.0
CB B:PHE223 4.6 24.5 1.0
HA B:PHE223 4.7 26.7 1.0
O B:ARG222 4.7 22.4 1.0
HB3 B:ASP263 4.8 52.1 1.0
H B:ARG222 4.8 26.4 1.0
HG23 B:ILE259 4.8 49.0 1.0
HA B:LEU220 4.9 30.7 1.0
HB2 B:ASN221 4.9 33.1 1.0
CA B:ALA266 4.9 31.5 1.0
H B:ALA266 4.9 36.6 1.0
C B:ALA266 4.9 31.4 1.0
CA B:THR224 4.9 26.8 1.0
HB2 B:ASP263 4.9 52.1 1.0
HA B:ASN221 5.0 32.0 1.0
N B:MET264 5.0 30.3 1.0

Sodium binding site 2 out of 2 in 8p57

Go back to Sodium Binding Sites List in 8p57
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 75 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 75 Micromolar X77. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:34.4
occ:1.00
HH B:TYR101 1.7 28.1 1.0
OD2 B:ASP33 2.4 35.9 1.0
OH B:TYR101 2.5 23.4 1.0
O B:HOH662 2.6 27.9 1.0
HB2 B:ASP33 2.6 30.9 1.0
HE1 B:TYR101 3.1 28.6 1.0
CG B:ASP33 3.2 36.3 1.0
CB B:ASP33 3.3 25.7 1.0
CZ B:TYR101 3.5 21.7 1.0
CE1 B:TYR101 3.6 23.9 1.0
HB3 B:ASP33 3.8 30.9 1.0
HB3 B:LEU32 4.0 21.9 1.0
O B:HOH607 4.1 36.8 1.0
O B:LEU32 4.1 19.4 1.0
HB2 B:LEU32 4.3 21.9 1.0
C B:LEU32 4.3 19.1 1.0
OD1 B:ASP33 4.4 36.7 1.0
N B:ASP33 4.5 23.0 1.0
CA B:ASP33 4.5 23.9 1.0
CB B:LEU32 4.6 18.2 1.0
HG21 B:THR98 4.6 29.6 1.0
CE2 B:TYR101 4.8 20.3 1.0
OH B:TYR37 4.8 21.8 1.0
H B:ASP33 4.9 27.6 1.0
CD1 B:TYR101 5.0 22.2 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: Wed Oct 9 12:52:33 2024

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