Zinc in PDB 5sm7: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1247413608

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1247413608, PDB code: 5sm7 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)	22.32 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.595, 67.858, 138.609, 90, 90, 90
R / Rfree (%)	23.7 / 26.8

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1247413608 (pdb code 5sm7). 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 Z1247413608, PDB code: 5sm7:
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 Z1247413608


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 Z1247413608 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:37.6 occ:1.00 ND1 D:HIS264 2.0 49.3 1.0 NE2 D:HIS257 2.1 43.3 1.0 SG D:CYS279 2.2 35.1 1.0 SG D:CYS261 2.4 49.0 1.0 CE1 D:HIS264 2.9 49.7 1.0 CD2 D:HIS257 3.0 41.9 1.0 CG D:HIS264 3.1 48.5 1.0 CB D:CYS279 3.1 33.4 1.0 CB D:CYS261 3.1 47.8 1.0 CE1 D:HIS257 3.2 43.0 1.0 CB D:HIS264 3.5 50.2 1.0 NE2 D:HIS264 4.1 49.4 1.0 CG D:HIS257 4.2 41.5 1.0 CD2 D:HIS264 4.2 48.5 1.0 ND1 D:HIS257 4.3 43.1 1.0 N D:HIS264 4.3 51.9 1.0 CA D:HIS264 4.5 52.2 1.0 CA D:CYS279 4.6 33.2 1.0 CA D:CYS261 4.6 48.3 1.0 N D:ASP415 4.6 37.1 1.0 SG D:CYS414 4.9 39.4 0.6 CA D:CYS414 5.0 36.7 0.4

Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1247413608


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 Z1247413608 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:43.9 occ:1.00 ND1 D:HIS487 2.2 43.7 1.0 SG D:CYS484 2.2 41.2 1.0 SG D:CYS452 2.3 50.4 1.0 SG D:CYS477 2.4 44.4 1.0 CB D:CYS452 3.1 54.2 1.0 CE1 D:HIS487 3.1 43.6 1.0 CB D:CYS477 3.2 40.8 1.0 CG D:HIS487 3.2 41.8 1.0 CB D:CYS484 3.3 41.4 1.0 CB D:HIS487 3.5 39.8 1.0 CA D:CYS452 3.7 55.7 1.0 N D:CYS484 4.0 41.5 1.0 CA D:CYS484 4.2 41.4 1.0 NE2 D:HIS487 4.3 44.0 1.0 CD2 D:HIS487 4.3 43.1 1.0 N D:CYS477 4.3 40.0 1.0 CA D:CYS477 4.4 40.1 1.0 N D:HIS487 4.5 40.5 1.0 N D:CYS452 4.5 54.2 1.0 CA D:HIS487 4.6 40.1 1.0 CB D:THR475 4.8 39.4 1.0 O D:CYS484 4.9 42.8 1.0 C D:CYS484 4.9 42.4 1.0 OG1 D:THR475 4.9 39.3 1.0 C D:CYS452 4.9 59.0 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 Z1247413608


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 Z1247413608 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:50.3 occ:1.00 ND1 D:HIS229 2.0 47.4 1.0 SG D:CYS207 2.3 56.7 1.0 SG D:CYS226 2.4 48.4 1.0 SG D:CYS210 2.5 53.2 1.0 CE1 D:HIS229 2.9 47.5 1.0 CB D:CYS207 3.0 55.9 1.0 CG D:HIS229 3.2 45.5 1.0 CB D:CYS226 3.4 43.7 1.0 CB D:CYS210 3.5 53.7 1.0 CB D:HIS229 3.6 43.3 1.0 N D:CYS210 3.8 54.7 1.0 N D:CYS226 3.9 43.3 1.0 NE2 D:HIS229 4.1 47.8 1.0 CA D:CYS210 4.1 54.1 1.0 CD2 D:HIS229 4.2 46.8 1.0 CA D:CYS226 4.3 42.6 1.0 NH1 D:ARG212 4.3 51.9 1.0 C D:LEU209 4.4 55.7 1.0 N D:HIS229 4.4 42.2 1.0 CA D:CYS207 4.5 56.0 1.0 C D:CYS210 4.7 54.7 1.0 CB D:LEU209 4.7 56.9 1.0 CD D:ARG212 4.7 49.1 1.0 CA D:HIS229 4.7 42.5 1.0 CB D:ARG212 4.8 48.2 1.0 N D:LEU209 4.8 56.5 1.0 CA D:LEU209 4.9 56.4 1.0 O D:CYS210 4.9 55.5 1.0 CB D:HIS228 4.9 41.6 1.0 C D:CYS226 5.0 41.4 1.0

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