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Sodium in PDB 8p86: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm Mg-132, From An "Old" Crystal.

Enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm Mg-132, From An "Old" Crystal.

All present enzymatic activity of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm Mg-132, From An "Old" Crystal.:
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 5 Mm Mg-132, From An "Old" Crystal., PDB code: 8p86 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) 49.39 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.366, 99.351, 102.801, 90, 90, 90
R / Rfree (%) 17.3 / 19.7

Other elements in 8p86:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm Mg-132, From An "Old" Crystal. 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 5 Mm Mg-132, From An "Old" Crystal. (pdb code 8p86). 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 5 Mm Mg-132, From An "Old" Crystal., PDB code: 8p86:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8p86

Go back to Sodium Binding Sites List in 8p86
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 5 Mm Mg-132, From An "Old" Crystal.


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 5 Mm Mg-132, From An "Old" Crystal. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:37.5
occ:1.00
 OD1 A:ASP263 2.2 42.4 1.0
OD1 A:ASN221 2.2 33.0 1.0
O A:HOH503 2.4 37.8 1.0
O A:PHE223 2.4 32.5 1.0
O A:ASN221 2.6 32.9 1.0
O A:ASP263 2.8 34.3 1.0
HB3 A:ALA266 2.9 41.0 1.0
H A:PHE223 3.0 37.6 1.0
H A:ASN221 3.2 41.6 1.0
CG A:ASN221 3.3 34.6 1.0
C A:ASN221 3.3 35.8 1.0
CG A:ASP263 3.4 42.7 1.0
N A:PHE223 3.5 31.3 1.0
C A:PHE223 3.5 33.1 1.0
HA A:ASP263 3.5 43.0 1.0
C A:ASP263 3.6 37.9 1.0
H A:SER267 3.7 40.6 1.0
CB A:ALA266 3.8 34.2 1.0
OG A:SER267 3.9 41.4 1.0
N A:ASN221 3.9 34.6 1.0
HB1 A:ALA266 3.9 41.0 1.0
CA A:ASP263 3.9 35.8 1.0
CA A:PHE223 4.0 33.7 1.0
HB2 A:PHE223 4.0 44.1 1.0
CA A:ASN221 4.0 32.7 1.0
N A:SER267 4.1 33.8 1.0
HD21 A:ASN221 4.1 41.3 1.0
ND2 A:ASN221 4.1 34.4 1.0
C A:ARG222 4.2 34.6 1.0
N A:ARG222 4.2 30.3 1.0
CB A:ASN221 4.2 33.2 1.0
HG A:SER267 4.2 49.7 1.0
OD2 A:ASP263 4.2 46.1 1.0
CB A:ASP263 4.2 37.0 1.0
HB2 A:ALA266 4.4 41.0 1.0
HA A:THR224 4.4 42.6 1.0
C A:ALA266 4.5 36.7 1.0
HA A:ARG222 4.5 41.3 1.0
CB A:PHE223 4.5 36.8 1.0
CA A:ARG222 4.6 34.4 1.0
N A:THR224 4.6 31.7 1.0
H A:ALA266 4.6 39.9 1.0
HA A:SER267 4.6 44.3 1.0
CA A:ALA266 4.6 33.8 1.0
HA A:MET264 4.7 34.7 1.0
N A:MET264 4.7 32.4 1.0
HB2 A:ASN221 4.8 39.8 1.0
CA A:SER267 4.8 36.9 1.0
CB A:SER267 4.8 33.5 1.0
HA A:PHE223 4.8 40.4 1.0
HB3 A:ASP263 4.8 44.4 1.0
HB2 A:ASP263 4.9 44.4 1.0
H A:ARG222 4.9 36.4 1.0
HB3 A:ASN221 4.9 39.8 1.0
HA A:ASN221 4.9 39.3 1.0
HD22 A:ASN221 4.9 41.3 1.0
HA A:LEU220 5.0 37.7 1.0

Sodium binding site 2 out of 2 in 8p86

Go back to Sodium Binding Sites List in 8p86
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 5 Mm Mg-132, From An "Old" Crystal.


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 5 Mm Mg-132, From An "Old" Crystal. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:38.8
occ:1.00
 OD1 B:ASP263 2.0 47.6 1.0
OD1 B:ASN221 2.2 38.7 1.0
O B:PHE223 2.3 30.2 1.0
O B:HOH606 2.5 34.9 1.0
O B:ASN221 2.7 31.0 1.0
O B:ASP263 2.7 32.6 1.0
HB3 B:ALA266 2.9 46.2 1.0
CG B:ASP263 3.2 50.2 1.0
H B:ASN221 3.3 44.7 1.0
CG B:ASN221 3.3 40.5 1.0
C B:PHE223 3.3 36.5 1.0
HA B:ASP263 3.3 46.2 1.0
C B:ASN221 3.4 35.8 1.0
H B:PHE223 3.5 36.7 1.0
N B:PHE223 3.5 30.6 1.0
C B:ASP263 3.5 35.6 1.0
CA B:ASP263 3.8 38.5 1.0
CB B:ALA266 3.8 38.5 1.0
CA B:PHE223 3.9 34.9 1.0
HG B:SER267 3.9 48.9 1.0
HB1 B:ALA266 3.9 46.2 1.0
H B:SER267 4.0 44.3 1.0
N B:ASN221 4.0 37.2 1.0
HB2 B:PHE223 4.0 40.6 1.0
C B:ARG222 4.0 31.8 1.0
OD2 B:ASP263 4.0 49.8 1.0
OG B:SER267 4.0 40.7 1.0
CB B:ASP263 4.1 37.6 1.0
HD21 B:ASN221 4.1 43.8 1.0
CA B:ASN221 4.1 34.5 1.0
ND2 B:ASN221 4.2 36.5 1.0
N B:ARG222 4.2 32.1 1.0
CB B:ASN221 4.3 32.9 1.0
HB2 B:ALA266 4.3 46.2 1.0
N B:SER267 4.4 36.9 1.0
HA B:THR224 4.4 45.9 1.0
N B:THR224 4.5 34.1 1.0
CB B:PHE223 4.5 33.8 1.0
CA B:ARG222 4.6 31.5 1.0
HA B:ARG222 4.6 37.8 1.0
HB2 B:ASP263 4.6 45.1 1.0
N B:MET264 4.7 31.5 1.0
HA B:MET264 4.7 36.9 1.0
H B:ALA266 4.7 41.4 1.0
O B:ARG222 4.7 31.8 1.0
HB3 B:ASP263 4.7 45.1 1.0
HA B:PHE223 4.8 41.9 1.0
CA B:ALA266 4.8 36.4 1.0
HB2 B:ASN221 4.8 39.5 1.0
C B:ALA266 4.8 36.6 1.0
H B:ARG222 4.9 38.6 1.0
HD22 B:ASN221 5.0 43.8 1.0
HA B:LEU220 5.0 43.4 1.0
CB B:SER267 5.0 33.8 1.0
HB3 B:ASN221 5.0 39.5 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 12:54:30 2024

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