Sodium in PDB 7ntq: Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide, PDB code: 7ntq was solved by E.Dupre, V.Villeret, X.Hanoulle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.81 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.92, 52.91, 44.9, 90, 102.88, 90
R / Rfree (%)	17.1 / 21.3

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide (pdb code 7ntq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide, PDB code: 7ntq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide


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 Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:29.5 occ:1.00 H A:VAL148 2.0 16.3 1.0 HB3 A:LEU115 2.6 17.1 1.0 O A:LEU115 2.6 18.2 1.0 HA A:SER147 2.8 14.8 1.0 N A:VAL148 2.9 16.3 1.0 HG21 A:VAL148 3.0 17.5 1.0 HG23 A:VAL148 3.2 17.5 1.0 HE2 A:MET17 3.3 22.1 1.0 SD A:MET17 3.3 19.4 1.0 HE1 A:MET17 3.4 22.1 1.0 HD23 A:LEU115 3.4 18.5 1.0 CB A:LEU115 3.4 17.1 1.0 HB3 A:SER147 3.5 16.1 1.0 HG A:CYS117 3.5 21.0 0.0 CE A:MET17 3.5 22.1 1.0 CG2 A:VAL148 3.5 17.5 1.0 CA A:SER147 3.5 14.8 1.0 C A:LEU115 3.6 17.1 1.0 C A:SER147 3.7 15.8 1.0 SG A:CYS117 3.7 21.0 1.0 HG A:LEU115 3.7 17.9 1.0 HG3 A:MET17 3.7 18.5 1.0 H A:LEU115 3.7 17.0 1.0 O A:VAL148 3.8 17.6 1.0 HG11 A:VAL13 3.9 19.1 1.0 CA A:VAL148 3.9 15.2 1.0 CA A:LEU115 4.0 16.3 1.0 CB A:SER147 4.0 16.1 1.0 CG A:LEU115 4.0 17.9 1.0 HG13 A:VAL148 4.1 17.5 1.0 HB2 A:LEU115 4.1 17.1 1.0 CD2 A:LEU115 4.1 18.5 1.0 CG A:MET17 4.2 18.5 1.0 CB A:VAL148 4.2 16.6 1.0 HG12 A:VAL13 4.2 19.1 1.0 HB2 A:CYS117 4.3 18.2 1.0 N A:LEU115 4.3 17.0 1.0 C A:VAL148 4.4 16.8 1.0 HG22 A:VAL148 4.4 17.5 1.0 CG1 A:VAL13 4.4 19.1 1.0 HE3 A:MET17 4.5 22.1 1.0 OG A:SER147 4.5 17.5 1.0 HG2 A:MET17 4.6 18.5 1.0 CB A:CYS117 4.6 18.2 1.0 HD21 A:LEU115 4.7 18.5 1.0 CG1 A:VAL148 4.7 17.5 1.0 HG13 A:VAL13 4.7 19.1 1.0 O A:GLY146 4.7 17.3 1.0 HA A:VAL148 4.7 15.2 1.0 N A:ALA116 4.8 16.6 1.0 HD22 A:LEU115 4.8 18.5 1.0 HB2 A:SER147 4.8 16.1 1.0 H A:CYS117 4.8 17.6 1.0 N A:SER147 4.8 16.1 1.0 HA A:LEU115 4.9 16.3 1.0 O A:SER147 4.9 15.4 1.0 HA A:ALA116 4.9 16.9 1.0 HG A:SER147 5.0 17.5 0.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide


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 Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:26.8 occ:1.00 H A:GLY174 2.1 16.5 1.0 HA A:ALA173 2.5 17.1 1.0 HB2 A:TYR182 2.6 18.9 1.0 O A:PHE134 2.8 24.0 1.0 O A:TYR182 2.9 20.8 1.0 N A:GLY174 2.9 16.5 1.0 HD2 A:PHE185 3.1 20.9 1.0 O A:GLY174 3.2 16.6 1.0 CA A:ALA173 3.3 17.1 1.0 HB1 A:ALA173 3.3 17.8 1.0 HB2 A:ALA173 3.4 17.8 1.0 CB A:TYR182 3.5 18.9 1.0 HD2 A:PHE181 3.5 18.6 1.0 CB A:ALA173 3.5 17.8 1.0 H A:TYR182 3.6 18.4 1.0 C A:ALA173 3.6 16.9 1.0 C A:TYR182 3.7 19.2 1.0 HB3 A:TYR182 3.7 18.9 1.0 HA A:THR135 3.8 19.7 1.0 CD2 A:PHE185 3.8 20.9 1.0 HE1 A:TYR161 3.9 18.4 1.0 CA A:TYR182 4.0 18.5 1.0 C A:GLY174 4.0 16.8 1.0 HE2 A:PHE185 4.0 20.6 1.0 CA A:GLY174 4.0 15.5 1.0 N A:TYR182 4.0 18.4 1.0 C A:PHE134 4.1 21.7 1.0 HB3 A:PHE134 4.1 23.4 1.0 HD2 A:TYR182 4.2 18.4 1.0 HB2 A:PHE185 4.3 20.1 1.0 CE2 A:PHE185 4.3 20.6 1.0 CD2 A:PHE181 4.4 18.6 1.0 HH A:TYR161 4.4 15.7 0.0 HB3 A:ALA173 4.5 17.8 1.0 O A:HIS172 4.5 19.3 1.0 N A:ALA173 4.5 16.8 1.0 HE1 A:MET130 4.6 23.5 1.0 CG A:TYR182 4.6 17.5 1.0 HA2 A:GLY174 4.6 15.5 1.0 HB3 A:PHE181 4.7 17.6 1.0 HA3 A:GLY174 4.7 15.5 1.0 CA A:THR135 4.7 19.7 1.0 HE2 A:PHE181 4.8 18.3 1.0 CE1 A:TYR161 4.8 18.4 1.0 CD2 A:TYR182 4.8 18.4 1.0 CG A:PHE185 4.8 19.4 1.0 N A:THR135 4.8 21.3 1.0 CB A:PHE134 4.9 23.4 1.0 O A:ALA173 4.9 15.4 1.0 N A:GLY183 4.9 19.0 1.0 HA3 A:GLY183 4.9 20.2 1.0 HA A:TYR182 4.9 18.5 1.0 C A:HIS172 4.9 17.4 1.0 HB2 A:PHE134 5.0 23.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N- (Pyridin-3-Ylmethyl)Thioformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:23.8 occ:1.00 H A:PHE291 2.0 16.9 1.0 HA A:ASP289 2.7 16.9 1.0 HB2 A:PHE291 2.7 19.8 1.0 HB2 A:TRP207 2.7 16.3 1.0 O A:GLU288 2.8 17.8 1.0 HB3 A:ASN203 2.8 16.5 1.0 O A:ASN203 2.8 16.7 1.0 HD2 A:PHE291 2.8 19.7 1.0 N A:PHE291 2.8 16.9 1.0 O A:PHE291 3.1 18.5 1.0 HB3 A:TRP207 3.3 16.3 1.0 CA A:ASP289 3.3 16.9 1.0 H A:GLU290 3.3 18.6 1.0 C A:ASP289 3.3 17.5 1.0 C A:ASN203 3.3 16.2 1.0 N A:GLU290 3.4 18.6 1.0 C A:GLU288 3.4 17.8 1.0 CB A:PHE291 3.4 19.8 1.0 CB A:TRP207 3.4 16.3 1.0 CA A:PHE291 3.5 19.1 1.0 N A:ASP289 3.6 18.0 1.0 HA A:VAL204 3.6 14.8 1.0 CD2 A:PHE291 3.6 19.7 1.0 CB A:ASN203 3.7 16.5 1.0 C A:PHE291 3.8 19.1 1.0 H A:TRP207 3.8 15.7 1.0 C A:GLU290 3.9 19.9 1.0 N A:VAL204 4.0 15.3 1.0 CG A:PHE291 4.0 19.3 1.0 CA A:ASN203 4.0 15.8 1.0 HB2 A:ASN203 4.0 16.5 1.0 O A:ASP289 4.0 18.4 1.0 HB2 A:GLU288 4.1 22.2 1.0 HB3 A:GLU288 4.1 22.2 1.0 HA A:ASN203 4.1 15.8 1.0 CG A:TRP207 4.2 17.2 1.0 HB3 A:PHE291 4.2 19.8 1.0 CA A:GLU290 4.2 20.3 1.0 CA A:VAL204 4.3 14.8 1.0 H A:ASP289 4.3 18.0 1.0 HA A:PHE291 4.4 19.1 1.0 N A:TRP207 4.4 15.7 1.0 CB A:GLU288 4.5 22.2 1.0 HB3 A:ALA206 4.5 17.5 1.0 CA A:TRP207 4.5 16.4 1.0 HA A:GLU290 4.6 20.3 1.0 CA A:GLU288 4.6 19.7 1.0 H A:VAL204 4.6 15.3 1.0 CB A:ASP289 4.7 18.0 1.0 HD22 A:ASN203 4.7 17.5 1.0 HD1 A:TRP207 4.7 18.6 1.0 CD1 A:TRP207 4.7 18.6 1.0 CG A:ASN203 4.8 16.1 1.0 HB2 A:ASP289 4.8 18.0 1.0 HA A:TRP207 4.8 16.4 1.0 CE2 A:PHE291 4.8 20.4 1.0 HG21 A:VAL204 4.9 15.3 1.0 C A:VAL204 5.0 15.1 1.0 HE2 A:PHE291 5.0 20.4 1.0

E.Dupre, V.Villeret, X.Hanoulle. Crystal Structure of the Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl)Thioformamide To Be Published.