Sodium in PDB 9ez6: Complex of A Mutant of the Sars-Cov-2 Main Protease Mpro with the NSP14/15 Substrate Peptide.

The structure of Complex of A Mutant of the Sars-Cov-2 Main Protease Mpro with the NSP14/15 Substrate Peptide., PDB code: 9ez6 was solved by R.Battistutta, E.Fornasier, G.Giachin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.95 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.802, 99.032, 100.841, 90, 90, 90
R / Rfree (%)	19.5 / 22.8

The binding sites of Sodium atom in the Complex of A Mutant of the Sars-Cov-2 Main Protease Mpro with the NSP14/15 Substrate Peptide. (pdb code 9ez6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Complex of A Mutant of the Sars-Cov-2 Main Protease Mpro with the NSP14/15 Substrate Peptide., PDB code: 9ez6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Complex of A Mutant of the Sars-Cov-2 Main Protease Mpro with the NSP14/15 Substrate Peptide.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of A Mutant of the Sars-Cov-2 Main Protease Mpro with the NSP14/15 Substrate Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na414 b:63.6 occ:1.00 OD1 A:ASP263 2.0 60.5 1.0 OD1 A:ASN221 2.0 64.5 1.0 O A:PHE223 2.3 54.5 1.0 O A:ASN221 2.3 55.2 1.0 O A:HOH507 2.5 53.9 1.0 H A:PHE223 3.0 69.7 1.0 O A:ASP263 3.0 48.5 1.0 C A:ASN221 3.1 60.6 1.0 H A:ASN221 3.1 67.7 1.0 CG A:ASP263 3.2 65.0 1.0 HB3 A:ALA266 3.2 66.3 1.0 CG A:ASN221 3.2 48.0 1.0 N A:PHE223 3.3 58.1 1.0 C A:PHE223 3.4 56.6 1.0 HA A:ASP263 3.6 60.9 1.0 C A:ASP263 3.8 49.4 1.0 N A:ASN221 3.8 56.4 1.0 CA A:ASN221 3.9 56.2 1.0 CA A:PHE223 3.9 57.1 1.0 C A:ARG222 3.9 58.9 1.0 OD2 A:ASP263 3.9 61.8 1.0 N A:ARG222 3.9 55.6 1.0 CA A:ASP263 4.0 50.7 1.0 CB A:ALA266 4.1 55.3 1.0 HB2 A:PHE223 4.1 73.9 1.0 CB A:ASN221 4.1 56.3 1.0 CB A:ASP263 4.2 51.2 1.0 HB1 A:ALA266 4.2 66.3 1.0 HA A:ARG222 4.2 66.7 1.0 HD21 A:ASN221 4.2 71.6 1.0 ND2 A:ASN221 4.2 59.7 1.0 CA A:ARG222 4.2 55.6 1.0 H A:SER267 4.2 56.5 1.0 OG A:SER267 4.3 54.7 1.0 HA A:THR224 4.4 66.9 1.0 N A:THR224 4.5 60.7 1.0 HB2 A:ALA266 4.6 66.3 1.0 CB A:PHE223 4.6 61.6 1.0 HB2 A:ASN221 4.6 67.5 1.0 N A:SER267 4.6 47.0 1.0 HG A:SER267 4.6 65.6 1.0 HB2 A:ASP263 4.6 61.5 1.0 H A:ARG222 4.6 66.7 1.0 O A:ARG222 4.7 68.5 1.0 HA A:PHE223 4.7 68.6 1.0 HA A:ASN221 4.8 67.5 1.0 HB3 A:ASN221 4.9 67.5 1.0 HB3 A:ASP263 4.9 61.5 1.0 C A:ALA266 5.0 47.9 1.0 N A:MET264 5.0 43.7 1.0

Sodium binding site 2 out of 2 in the Complex of A Mutant of the Sars-Cov-2 Main Protease Mpro with the NSP14/15 Substrate Peptide.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of A Mutant of the Sars-Cov-2 Main Protease Mpro with the NSP14/15 Substrate Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:59.0 occ:1.00 OD1 B:ASP263 2.0 64.9 1.0 OD1 B:ASN221 2.0 55.6 1.0 O B:HOH504 2.3 49.2 1.0 O B:ASP263 2.5 58.5 1.0 O B:PHE223 2.6 53.8 1.0 HB3 B:ALA266 2.7 76.1 1.0 O B:ASN221 2.7 56.2 1.0 H B:ASN221 3.0 68.6 1.0 CG B:ASN221 3.1 52.3 1.0 CG B:ASP263 3.2 64.6 1.0 OG B:SER267 3.3 63.9 1.0 C B:ASP263 3.3 55.8 1.0 H B:SER267 3.3 71.7 1.0 H B:PHE223 3.4 64.1 1.0 HA B:ASP263 3.4 64.3 1.0 C B:ASN221 3.5 56.2 1.0 HG B:SER267 3.6 76.6 1.0 CB B:ALA266 3.7 63.4 1.0 C B:PHE223 3.7 53.5 1.0 N B:PHE223 3.8 53.4 1.0 CA B:ASP263 3.8 53.5 1.0 N B:ASN221 3.8 57.2 1.0 N B:SER267 3.8 59.7 1.0 HD21 B:ASN221 3.8 68.2 1.0 HB1 B:ALA266 3.9 76.1 1.0 ND2 B:ASN221 3.9 56.8 1.0 CA B:ASN221 4.0 55.9 1.0 OD2 B:ASP263 4.1 66.5 1.0 CB B:ASP263 4.1 58.9 1.0 CB B:ASN221 4.1 62.0 1.0 HB2 B:PHE223 4.2 66.4 1.0 HB2 B:ALA266 4.2 76.1 1.0 CA B:PHE223 4.2 54.9 1.0 HA B:MET264 4.4 63.9 1.0 C B:ALA266 4.4 55.8 1.0 N B:MET264 4.4 53.8 1.0 H B:ALA266 4.4 68.0 1.0 CB B:SER267 4.4 51.3 1.0 C B:ARG222 4.4 54.0 1.0 N B:ARG222 4.5 51.2 1.0 CA B:ALA266 4.5 57.7 1.0 HA B:SER267 4.5 65.8 1.0 CA B:SER267 4.5 54.9 1.0 HA B:THR224 4.6 67.2 1.0 HB3 B:ASP263 4.6 70.7 1.0 HA B:LEU220 4.7 70.5 1.0 HB2 B:SER267 4.7 61.6 1.0 HB2 B:ASN221 4.7 74.4 1.0 HD22 B:ASN221 4.7 68.2 1.0 HB2 B:ASP263 4.7 70.7 1.0 HB3 B:ASN221 4.7 74.4 1.0 N B:ALA266 4.7 56.6 1.0 CB B:PHE223 4.8 55.3 1.0 N B:THR224 4.8 55.1 1.0 CA B:MET264 4.8 53.2 1.0 CA B:ARG222 4.9 53.0 1.0 HA B:ASN221 4.9 67.0 1.0 HA B:ARG222 5.0 63.6 1.0 C B:LEU220 5.0 51.8 1.0

E.Fornasier, S.Fabbian, H.Shehi, J.Enderle, B.Gatto, D.Volpin, B.Biondi, M.Bellanda, G.Giachin, A.Sosic, R.Battistutta. Allostery in Homodimeric Sars-Cov-2 Main Protease. Commun Biol V. 7 1435 2024.
ISSN: ESSN 2399-3642
PubMed: 39496839
DOI: 10.1038/S42003-024-07138-W