Zinc in PDB 5sl6: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z256709556

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z256709556, PDB code: 5sl6 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)	38.19 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.125, 67.928, 138.368, 90, 90, 90
R / Rfree (%)	23.5 / 29.3

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z256709556 (pdb code 5sl6). 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 Z256709556, PDB code: 5sl6:
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 Z256709556


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 Z256709556 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:47.7 occ:1.00 ND1 D:HIS264 2.0 55.9 1.0 SG D:CYS279 2.3 34.7 1.0 NE2 D:HIS257 2.3 45.9 1.0 SG D:CYS261 2.3 49.0 1.0 CB D:CYS261 2.8 48.3 1.0 CE1 D:HIS264 3.0 56.9 1.0 CG D:HIS264 3.1 54.2 1.0 CD2 D:HIS257 3.1 45.3 1.0 CB D:CYS279 3.3 35.7 1.0 CE1 D:HIS257 3.4 45.9 1.0 CB D:HIS264 3.4 52.8 1.0 NE2 D:HIS264 4.2 57.0 1.0 CD2 D:HIS264 4.2 55.7 1.0 N D:HIS264 4.2 51.6 1.0 CA D:CYS261 4.2 48.7 1.0 CG D:HIS257 4.3 44.6 1.0 ND1 D:HIS257 4.4 45.9 1.0 CA D:HIS264 4.4 52.5 1.0 N D:ASP415 4.6 36.2 1.0 CA D:CYS279 4.7 36.5 1.0 C D:CYS261 4.7 50.2 1.0 SG D:CYS414 4.8 39.9 0.6 O D:CYS261 4.9 50.6 1.0 O D:HOH860 4.9 31.4 1.0 CA D:CYS414 5.0 36.5 0.4 CA D:CYS414 5.0 36.7 0.6

Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z256709556


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 Z256709556 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:47.4 occ:1.00 SG D:CYS484 2.2 46.5 1.0 ND1 D:HIS487 2.2 45.6 1.0 SG D:CYS452 2.5 58.6 1.0 SG D:CYS477 2.6 46.9 1.0 CE1 D:HIS487 3.0 45.5 1.0 CB D:CYS477 3.1 42.6 1.0 CB D:CYS452 3.2 59.1 1.0 CG D:HIS487 3.3 43.9 1.0 CB D:CYS484 3.4 45.1 1.0 CB D:HIS487 3.7 43.4 1.0 CA D:CYS452 3.8 59.5 1.0 N D:CYS484 4.0 44.3 1.0 CA D:CYS484 4.2 44.8 1.0 NE2 D:HIS487 4.2 44.9 1.0 CA D:CYS477 4.3 42.0 1.0 N D:CYS477 4.3 41.9 1.0 CD2 D:HIS487 4.4 44.2 1.0 O D:HOH829 4.5 42.3 1.0 N D:CYS452 4.6 57.9 1.0 N D:HIS487 4.6 43.8 1.0 CA D:HIS487 4.8 43.4 1.0 O D:CYS484 4.8 46.7 1.0 CB D:THR475 4.9 41.5 1.0 C D:CYS484 4.9 46.0 1.0 OG1 D:THR475 5.0 42.4 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 Z256709556


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 Z256709556 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:50.2 occ:1.00 ND1 D:HIS229 2.0 44.8 1.0 SG D:CYS207 2.3 51.4 1.0 SG D:CYS210 2.4 49.8 1.0 SG D:CYS226 2.7 51.4 1.0 CE1 D:HIS229 2.8 45.5 1.0 CB D:CYS207 2.9 49.1 1.0 CG D:HIS229 3.2 42.9 1.0 CB D:CYS210 3.4 48.2 1.0 CB D:CYS226 3.6 45.3 1.0 CB D:HIS229 3.8 41.2 1.0 N D:CYS210 3.9 47.5 1.0 N D:CYS226 3.9 44.4 1.0 NE2 D:HIS229 4.0 45.4 1.0 CA D:CYS210 4.1 47.7 1.0 CD2 D:HIS229 4.3 44.0 1.0 CA D:CYS226 4.3 43.8 1.0 CA D:CYS207 4.4 49.1 1.0 C D:LEU209 4.4 48.0 1.0 N D:HIS229 4.4 41.5 1.0 NH1 D:ARG212 4.5 54.0 1.0 C D:CYS210 4.7 47.8 1.0 CD D:ARG212 4.7 50.3 1.0 CA D:HIS229 4.8 41.2 1.0 CB D:LEU209 4.8 49.3 1.0 N D:LEU209 4.8 49.0 1.0 CB D:ARG212 4.8 48.0 1.0 CA D:LEU209 4.9 48.6 1.0 CB D:HIS228 4.9 43.1 1.0 C D:CYS226 5.0 42.5 1.0

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