Sodium in PDB 8okl: Crystal Structure of F2F-2020185-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020185-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
3.4.22.69;

The structure of Crystal Structure of F2F-2020185-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okl 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)	41.30 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.976, 99.433, 104.002, 90, 90, 90
R / Rfree (%)	16.5 / 18.9

The structure of Crystal Structure of F2F-2020185-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of F2F-2020185-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 8okl). 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 F2F-2020185-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of F2F-2020185-01X 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-2020185-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:49.3 occ:1.00 OE1 A:GLU178 2.2 46.3 1.0 O A:HOH515 2.4 30.1 1.0 O A:HOH760 2.6 26.8 1.0 O A:HOH795 2.6 49.4 1.0 O A:HOH810 2.9 43.5 1.0 CD A:GLU178 2.9 43.3 1.0 HB2 A:GLU178 3.1 24.1 1.0 HB2 A:ARG105 3.2 25.0 1.0 HG3 A:GLU178 3.3 33.3 1.0 OD2 A:ASP176 3.4 21.4 1.0 CG A:GLU178 3.5 27.8 1.0 CB A:GLU178 3.7 20.1 1.0 OE2 A:GLU178 3.8 55.0 1.0 CG A:ASP176 4.0 18.8 1.0 HD2 A:ARG105 4.0 21.8 1.0 CB A:ARG105 4.2 20.8 1.0 HB3 A:GLU178 4.2 24.1 1.0 HB3 A:ARG105 4.3 25.0 1.0 OD1 A:ASP176 4.3 15.6 1.0 H A:GLU178 4.3 19.3 1.0 HB2 A:ASP176 4.4 19.2 1.0 HG2 A:GLU178 4.4 33.3 1.0 H A:ARG105 4.6 18.2 1.0 O A:HOH691 4.6 27.6 1.0 O A:HOH717 4.7 45.6 1.0 CB A:ASP176 4.8 16.0 1.0 CD A:ARG105 4.8 18.1 1.0 OD1 A:ASN180 4.8 30.9 1.0 HD3 A:ARG105 4.9 21.8 1.0 N A:ARG105 4.9 15.2 1.0 N A:GLU178 5.0 16.1 1.0 CA A:GLU178 5.0 18.5 1.0 CG A:ARG105 5.0 16.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of F2F-2020185-01X 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 2 of Crystal Structure of F2F-2020185-01X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:26.5 occ:1.00 OD1 B:ASP263 2.1 36.5 1.0 OD1 B:ASN221 2.2 23.8 1.0 O B:PHE223 2.3 22.2 1.0 O B:HOH532 2.4 23.0 1.0 O B:ASN221 2.7 23.9 1.0 O B:ASP263 2.8 23.5 1.0 HB3 B:ALA266 3.0 32.2 1.0 H B:PHE223 3.0 26.2 1.0 H B:ASN221 3.2 28.6 1.0 CG B:ASP263 3.3 30.2 1.0 CG B:ASN221 3.3 25.8 1.0 C B:PHE223 3.4 22.0 1.0 C B:ASN221 3.4 20.8 1.0 N B:PHE223 3.4 21.9 1.0 HA B:ASP263 3.5 28.1 1.0 C B:ASP263 3.6 20.4 1.0 CB B:ALA266 3.9 26.8 1.0 N B:ASN221 3.9 23.9 1.0 CA B:PHE223 3.9 22.5 1.0 CA B:ASP263 3.9 23.4 1.0 HB1 B:ALA266 4.0 32.2 1.0 H B:SER267 4.0 26.6 1.0 HB2 B:PHE223 4.0 28.1 1.0 HG B:SER267 4.0 30.7 1.0 CA B:ASN221 4.0 19.2 1.0 HD21 B:ASN221 4.1 29.3 1.0 C B:ARG222 4.1 22.5 1.0 ND2 B:ASN221 4.1 24.4 1.0 OD2 B:ASP263 4.1 37.9 1.0 CB B:ASP263 4.2 25.9 1.0 N B:ARG222 4.2 21.1 1.0 OG B:SER267 4.2 25.6 1.0 CB B:ASN221 4.2 21.9 1.0 HA B:THR224 4.3 29.1 1.0 N B:SER267 4.4 22.2 1.0 HB2 B:ALA266 4.4 32.2 1.0 CB B:PHE223 4.5 23.4 1.0 N B:THR224 4.5 23.9 1.0 CA B:ARG222 4.6 22.1 1.0 HA B:ARG222 4.6 26.5 1.0 HB2 B:ASN221 4.7 26.3 1.0 HA B:PHE223 4.7 27.0 1.0 HB2 B:ASP263 4.7 31.1 1.0 N B:MET264 4.7 19.4 1.0 H B:ALA266 4.8 29.0 1.0 C B:ALA266 4.8 22.0 1.0 O B:ARG222 4.8 23.4 1.0 HA B:MET264 4.8 23.0 1.0 CA B:ALA266 4.8 26.0 1.0 H B:ARG222 4.8 25.3 1.0 HB3 B:ASP263 4.8 31.1 1.0 HA B:LEU220 4.9 24.3 1.0 HD22 B:ASN221 4.9 29.3 1.0 HB3 B:ASN221 4.9 26.3 1.0 HA B:ASN221 4.9 23.1 1.0 CA B:THR224 4.9 24.2 1.0

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