Zinc in PDB 9fws: Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258

All present enzymatic activity of Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258:
2.1.1.56;

The structure of Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258, PDB code: 9fws was solved by T.Krojer, F.Kozielski, C.Sele, M.Nyblom, S.Z.Fisher, W.Knecht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.26 / 1.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.042, 100.035, 51.384, 90, 114.83, 90
R / Rfree (%)	19.2 / 21.3

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258 (pdb code 9fws). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258, PDB code: 9fws:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:19.4 occ:1.00 NE2 A:HIS83 2.0 20.0 1.0 SG A:CYS74 2.3 18.9 1.0 SG A:CYS77 2.3 18.9 1.0 SG A:CYS90 2.3 20.2 1.0 CE1 A:HIS83 3.0 19.6 1.0 CD2 A:HIS83 3.1 20.0 1.0 CB A:CYS74 3.1 17.5 1.0 CB A:CYS90 3.2 23.8 1.0 CB A:CYS77 3.4 17.9 1.0 N A:CYS77 3.6 17.7 1.0 CA A:CYS77 3.9 17.3 1.0 CG A:HIS83 4.2 19.1 1.0 ND1 A:HIS83 4.2 19.5 1.0 O A:HOH439 4.4 39.2 1.0 O A:HOH370 4.4 24.6 1.0 CA A:CYS90 4.4 24.8 1.0 C A:TYR76 4.4 17.8 1.0 CB A:TYR76 4.4 17.7 1.0 CA A:CYS74 4.5 16.9 1.0 O A:CYS74 4.8 16.4 1.0 CA A:TYR76 4.8 17.1 1.0 C A:CYS74 4.9 15.8 1.0 CB A:LYS93 4.9 18.3 1.0 N A:LYS93 4.9 18.9 1.0 N A:TYR76 4.9 16.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:29.6 occ:1.00 SG A:CYS130 2.3 32.3 1.0 SG A:CYS117 2.3 28.8 1.0 SG A:CYS128 2.3 30.6 1.0 SG A:CYS120 2.3 27.7 1.0 CB A:CYS117 3.1 28.4 1.0 CB A:CYS130 3.3 36.1 1.0 CB A:CYS120 3.4 28.1 1.0 CB A:CYS128 3.5 31.8 1.0 N A:CYS130 3.6 37.3 1.0 N A:CYS120 3.8 29.2 1.0 N A:SER129 3.9 34.7 1.0 CA A:CYS128 4.0 32.3 1.0 CA A:CYS130 4.1 37.7 1.0 CA A:CYS120 4.2 28.0 1.0 NZ A:LYS124 4.2 46.3 1.0 C A:CYS128 4.3 33.9 1.0 CA A:CYS117 4.5 28.5 1.0 C A:SER129 4.6 37.0 1.0 OG A:SER129 4.7 36.6 1.0 CB A:VAL119 4.7 34.0 1.0 CA A:SER129 4.8 35.3 1.0 C A:VAL119 4.8 31.2 1.0 C A:CYS120 5.0 27.9 1.0 CE A:LYS124 5.0 44.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:29.5 occ:1.00 NE2 B:HIS257 2.0 30.4 1.0 ND1 B:HIS264 2.1 36.5 1.0 SG B:CYS261 2.3 32.9 1.0 SG B:CYS279 2.3 27.7 1.0 CE1 B:HIS264 3.0 36.9 1.0 CE1 B:HIS257 3.0 30.9 1.0 CB B:CYS261 3.1 37.6 1.0 CD2 B:HIS257 3.1 28.6 1.0 CG B:HIS264 3.1 36.9 1.0 CB B:CYS279 3.3 24.2 1.0 CB B:HIS264 3.5 41.1 1.0 O B:HOH617 4.1 46.3 1.0 CG B:HIS257 4.2 29.1 1.0 ND1 B:HIS257 4.2 30.1 1.0 NE2 B:HIS264 4.2 37.4 1.0 CD2 B:HIS264 4.2 37.0 1.0 N B:HIS264 4.4 45.7 1.0 O B:HOH550 4.4 30.1 1.0 CA B:CYS261 4.5 40.1 1.0 CA B:HIS264 4.5 44.0 1.0 CA B:CYS279 4.7 23.4 1.0 CG2 B:VAL263 4.8 50.2 1.0 C B:CYS261 4.9 42.5 1.0 CE1 B:HIS283 4.9 33.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:33.0 occ:1.00 ND1 B:HIS229 1.8 30.5 1.0 SG B:CYS207 2.2 32.9 1.0 SG B:CYS210 2.3 36.0 1.0 SG B:CYS226 2.3 29.1 1.0 CE1 B:HIS229 2.4 34.6 1.0 CB B:CYS207 3.0 35.1 1.0 CG B:HIS229 3.1 32.0 1.0 CB B:CYS226 3.4 25.8 1.0 CB B:CYS210 3.5 39.5 1.0 NE2 B:HIS229 3.7 36.2 1.0 CB B:HIS229 3.8 30.2 1.0 N B:CYS210 3.9 42.1 1.0 N B:CYS226 3.9 24.8 1.0 CD2 B:HIS229 4.0 35.3 1.0 CA B:CYS210 4.2 40.3 1.0 NH1 B:ARG212 4.2 44.0 1.0 CA B:CYS226 4.3 25.2 1.0 C B:LEU209 4.3 44.4 1.0 CA B:CYS207 4.5 35.5 1.0 N B:LEU209 4.5 46.3 1.0 N B:HIS229 4.6 28.2 1.0 CD B:ARG212 4.6 39.5 1.0 CB B:ARG212 4.7 34.9 1.0 CB B:LEU209 4.7 46.5 1.0 C B:CYS210 4.7 40.4 1.0 CA B:LEU209 4.7 45.9 1.0 CA B:HIS229 4.9 28.9 1.0 O B:CYS210 4.9 40.8 1.0 O B:LEU209 4.9 45.2 1.0 C B:CYS226 5.0 23.9 1.0 C B:CYS207 5.0 40.3 1.0 CG B:ARG212 5.0 36.7 1.0

T.Krojer, F.Kozielski, C.Sele, M.Nyblom, S.Z.Fisher, W.Knecht. Crystal Structure of Sars-Cov-2 NSP10-NSP14 (Exon) in Complex with VT00258 To Be Published.