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Sodium in PDB 8okm: Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

Enzymatic activity of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okm 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) 41.33 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.025, 100.036, 104.065, 90, 90, 90
R / Rfree (%) 16.3 / 18.7

Other elements in 8okm:

The structure of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Bromine (Br) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 8okm). 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 F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okm:

Sodium binding site 1 out of 1 in 8okm

Go back to Sodium Binding Sites List in 8okm
Sodium binding site 1 out of 1 in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


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 F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:28.3
occ:1.00
 OD1 B:ASP263 2.1 35.3 1.0
OD1 B:ASN221 2.3 25.6 1.0
O B:PHE223 2.3 22.3 1.0
O B:HOH526 2.4 26.8 1.0
O B:ASN221 2.8 25.1 1.0
O B:ASP263 2.8 26.1 1.0
H B:PHE223 3.0 27.1 1.0
HB3 B:ALA266 3.0 33.6 1.0
H B:ASN221 3.2 30.5 1.0
CG B:ASP263 3.2 37.8 1.0
C B:PHE223 3.4 23.3 1.0
HA B:ASP263 3.4 33.4 1.0
N B:PHE223 3.4 22.6 1.0
CG B:ASN221 3.4 27.2 1.0
C B:ASN221 3.4 23.5 1.0
C B:ASP263 3.6 26.3 1.0
CA B:ASP263 3.9 27.9 1.0
CA B:PHE223 3.9 23.5 1.0
N B:ASN221 3.9 25.4 1.0
CB B:ALA266 3.9 28.0 1.0
H B:SER267 4.0 33.1 1.0
O B:HOH524 4.0 46.4 1.0
HB2 B:PHE223 4.0 28.2 1.0
HB1 B:ALA266 4.1 33.6 1.0
C B:ARG222 4.1 23.0 1.0
CA B:ASN221 4.1 23.7 1.0
OD2 B:ASP263 4.1 43.0 1.0
CB B:ASP263 4.1 29.9 1.0
OG B:SER267 4.1 28.7 1.0
HD21 B:ASN221 4.2 32.2 1.0
HG B:SER267 4.2 34.5 1.0
N B:ARG222 4.2 21.7 1.0
ND2 B:ASN221 4.3 26.8 1.0
HA B:THR224 4.3 33.8 1.0
CB B:ASN221 4.3 24.9 1.0
N B:SER267 4.4 27.6 1.0
HB2 B:ALA266 4.5 33.6 1.0
N B:THR224 4.5 24.4 1.0
CB B:PHE223 4.6 23.5 1.0
CA B:ARG222 4.6 22.5 1.0
HA B:ARG222 4.6 27.0 1.0
HB2 B:ASP263 4.7 35.9 1.0
H B:ALA266 4.7 30.4 1.0
HA B:PHE223 4.7 28.1 1.0
N B:MET264 4.7 25.0 1.0
HB3 B:ASP263 4.8 35.9 1.0
O B:ARG222 4.8 23.9 1.0
HA B:MET264 4.8 28.3 1.0
HB2 B:ASN221 4.8 29.9 1.0
C B:ALA266 4.8 26.6 1.0
CA B:ALA266 4.9 26.2 1.0
H B:ARG222 4.9 26.0 1.0
CA B:THR224 4.9 28.1 1.0
HA B:LEU220 4.9 30.4 1.0
HG23 B:ILE259 5.0 31.6 1.0
HA B:ASN221 5.0 28.5 1.0

Reference:

I.Stefanelli, A.Corona, C.Cerchia, E.Cassese, S.Improta, E.Costanzi, S.Pelliccia, S.Morasso, F.Esposito, A.Paulis, S.Scognamiglio, F.S.Di Leva, P.Storici, M.Brindisi, E.Tramontano, R.Cannalire, V.Summa. Broad-Spectrum Coronavirus 3C-Like Protease Peptidomimetic Inhibitors Effectively Block Sars-Cov-2 Replication in Cells: Design, Synthesis, Biological Evaluation, and X-Ray Structure Determination. Eur.J.Med.Chem. V. 253 15311 2023.
ISSN: ISSN 0223-5234
PubMed: 37043904
DOI: 10.1016/J.EJMECH.2023.115311
Page generated: Wed Oct 9 12:45:58 2024

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