Zinc in PDB 5sm0: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176, PDB code: 5sm0 was solved by N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.28 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.669, 68.214, 138.551, 90, 90, 90
R / Rfree (%)	23.6 / 27.3

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176 (pdb code 5sm0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176, PDB code: 5sm0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:42.1 occ:1.00 ND1 D:HIS264 2.0 48.4 1.0 NE2 D:HIS257 2.2 43.7 1.0 SG D:CYS279 2.3 36.1 1.0 SG D:CYS261 2.4 49.3 1.0 CE1 D:HIS264 2.9 48.8 1.0 CD2 D:HIS257 3.0 43.2 1.0 CB D:CYS261 3.1 46.4 1.0 CG D:HIS264 3.1 47.3 1.0 CB D:CYS279 3.2 35.7 1.0 CE1 D:HIS257 3.3 43.9 1.0 CB D:HIS264 3.5 49.0 1.0 NE2 D:HIS264 4.1 48.7 1.0 CG D:HIS257 4.2 43.0 1.0 CD2 D:HIS264 4.2 47.7 1.0 N D:HIS264 4.3 50.8 1.0 ND1 D:HIS257 4.3 44.1 1.0 CA D:HIS264 4.5 50.6 1.0 CA D:CYS261 4.5 46.2 1.0 N D:ASP415 4.6 38.4 1.0 CA D:CYS279 4.6 35.9 1.0 SG D:CYS414 4.9 45.4 0.6 C D:CYS261 4.9 46.7 1.0

Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:45.9 occ:1.00 ND1 D:HIS487 2.2 40.2 1.0 SG D:CYS484 2.2 40.6 1.0 SG D:CYS452 2.4 57.5 1.0 SG D:CYS477 2.4 48.6 1.0 CE1 D:HIS487 3.1 40.3 1.0 CB D:CYS452 3.2 58.4 1.0 CB D:CYS477 3.2 43.1 1.0 CG D:HIS487 3.2 39.2 1.0 CB D:CYS484 3.3 41.7 1.0 CB D:HIS487 3.6 39.2 1.0 CA D:CYS452 3.7 59.2 1.0 N D:CYS484 4.0 42.3 1.0 CA D:CYS484 4.2 42.2 1.0 NE2 D:HIS487 4.3 40.2 1.0 CD2 D:HIS487 4.3 39.5 1.0 N D:CYS477 4.4 42.9 1.0 CA D:CYS477 4.4 42.7 1.0 N D:HIS487 4.5 40.3 1.0 N D:CYS452 4.5 58.0 1.0 CA D:HIS487 4.7 39.9 1.0 CB D:THR475 4.8 41.7 1.0 OG1 D:THR475 4.9 42.6 1.0 O D:HOH751 4.9 41.5 1.0 C D:CYS484 4.9 42.9 1.0 O D:CYS484 5.0 43.2 1.0

Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32665176 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:51.6 occ:1.00 ND1 D:HIS229 2.0 48.3 1.0 SG D:CYS207 2.3 54.1 1.0 SG D:CYS210 2.4 57.4 1.0 SG D:CYS226 2.5 50.7 1.0 CE1 D:HIS229 2.8 49.0 1.0 CB D:CYS207 3.0 54.1 1.0 CG D:HIS229 3.2 46.6 1.0 CB D:CYS210 3.4 55.1 1.0 CB D:CYS226 3.5 43.0 1.0 CB D:HIS229 3.7 44.1 1.0 N D:CYS210 3.7 54.8 1.0 N D:CYS226 4.0 41.7 1.0 CA D:CYS210 4.0 54.7 1.0 NE2 D:HIS229 4.0 49.0 1.0 CD2 D:HIS229 4.2 47.8 1.0 NH1 D:ARG212 4.2 59.0 1.0 CA D:CYS226 4.3 41.2 1.0 C D:LEU209 4.4 55.5 1.0 CA D:CYS207 4.5 54.6 1.0 N D:HIS229 4.5 42.4 1.0 C D:CYS210 4.6 55.0 1.0 CB D:LEU209 4.7 56.2 1.0 CB D:ARG212 4.7 50.9 1.0 CD D:ARG212 4.7 54.1 1.0 CA D:HIS229 4.8 43.1 1.0 CA D:LEU209 4.8 55.8 1.0 N D:LEU209 4.8 55.5 1.0 O D:CYS210 4.8 55.3 1.0 CB D:HIS228 4.9 42.0 1.0 CG D:ARG212 5.0 52.0 1.0

N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman. Pandda Analysis Group Deposition To Be Published.