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Sodium in PDB 8p87: Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm X77, 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 X77, 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 X77, 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 X77, From An "Old" Crystal., PDB code: 8p87 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) 50.57 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.848, 101.138, 104.258, 90, 90, 90
R / Rfree (%) 17 / 19.1

Other elements in 8p87:

The structure of Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm X77, From An "Old" Crystal. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

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 X77, From An "Old" Crystal. (pdb code 8p87). 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 Obtained in Presence of 5 Mm X77, From An "Old" Crystal., PDB code: 8p87:

Sodium binding site 1 out of 1 in 8p87

Go back to Sodium Binding Sites List in 8p87
Sodium binding site 1 out of 1 in the Crystal Structure of the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 Obtained in Presence of 5 Mm X77, 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 X77, From An "Old" Crystal. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:36.3
occ:1.00
 OD1 B:ASP263 2.1 49.0 1.0
O B:PHE223 2.3 30.7 1.0
OD1 B:ASN221 2.3 32.5 1.0
O B:HOH510 2.4 34.6 1.0
O B:ASN221 2.6 31.6 1.0
HB3 B:ALA266 3.0 46.0 1.0
H B:PHE223 3.1 32.4 1.0
O B:ASP263 3.1 38.2 1.0
H B:ASN221 3.2 42.0 1.0
C B:ASN221 3.3 31.4 1.0
CG B:ASP263 3.3 49.2 1.0
C B:PHE223 3.4 29.7 1.0
N B:PHE223 3.4 27.1 1.0
CG B:ASN221 3.4 35.7 1.0
HA B:ASP263 3.6 52.2 1.0
CB B:ALA266 3.9 38.4 1.0
N B:ASN221 3.9 35.0 1.0
C B:ASP263 3.9 41.0 1.0
CA B:PHE223 3.9 28.4 1.0
HB1 B:ALA266 4.0 46.0 1.0
C B:ARG222 4.0 27.9 1.0
CA B:ASN221 4.0 32.5 1.0
CA B:ASP263 4.1 43.5 1.0
OD2 B:ASP263 4.1 52.6 1.0
HB2 B:PHE223 4.1 36.6 1.0
N B:ARG222 4.1 26.9 1.0
H B:SER267 4.2 42.6 1.0
HD21 B:ASN221 4.3 41.4 1.0
OG B:SER267 4.3 35.9 1.0
ND2 B:ASN221 4.3 34.5 1.0
CB B:ASN221 4.3 33.4 1.0
CB B:ASP263 4.3 49.0 1.0
HB2 B:ALA266 4.3 46.0 1.0
HA B:THR224 4.3 41.2 1.0
CA B:ARG222 4.5 27.9 1.0
HA B:ARG222 4.5 33.4 1.0
O B:HOH632 4.5 49.5 1.0
N B:THR224 4.5 30.2 1.0
N B:SER267 4.6 35.5 1.0
HG22 B:THR224 4.6 56.7 1.0
CB B:PHE223 4.6 30.5 1.0
HG B:SER267 4.6 43.1 1.0
O B:ARG222 4.7 28.9 1.0
HA B:PHE223 4.7 34.0 1.0
H B:ARG222 4.8 32.1 1.0
HB2 B:ASN221 4.8 40.1 1.0
HG23 B:ILE259 4.8 60.6 1.0
HA B:LEU220 4.9 38.7 1.0
C B:ALA266 4.9 38.4 1.0
HB3 B:ASP263 4.9 58.8 1.0
CA B:ALA266 4.9 35.2 1.0
H B:ALA266 4.9 46.6 1.0
HA B:ASN221 4.9 39.1 1.0
CA B:THR224 5.0 34.3 1.0
HG23 B:THR224 5.0 56.7 1.0
HB2 B:ASP263 5.0 58.8 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 12:54:33 2024

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