Zinc in PDB 5sl9: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z54571979

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z54571979, PDB code: 5sl9 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)	69.20 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.636, 68.494, 138.401, 90, 90, 90
R / Rfree (%)	27.1 / 29.5

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z54571979 (pdb code 5sl9). 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 Z54571979, PDB code: 5sl9:
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 Z54571979


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 Z54571979 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:39.4 occ:1.00 ND1 D:HIS264 2.0 47.3 1.0 NE2 D:HIS257 2.2 46.0 1.0 SG D:CYS279 2.3 36.9 1.0 SG D:CYS261 2.4 42.6 1.0 CE1 D:HIS264 2.9 47.3 1.0 CD2 D:HIS257 3.0 44.8 1.0 CB D:CYS261 3.1 45.9 1.0 CG D:HIS264 3.1 46.9 1.0 CB D:CYS279 3.1 34.0 1.0 CE1 D:HIS257 3.3 45.9 1.0 CB D:HIS264 3.5 49.0 1.0 NE2 D:HIS264 4.1 47.2 1.0 CD2 D:HIS264 4.2 46.7 1.0 CG D:HIS257 4.2 44.2 1.0 N D:HIS264 4.3 51.2 1.0 ND1 D:HIS257 4.4 45.8 1.0 CA D:HIS264 4.5 51.4 1.0 CA D:CYS261 4.5 47.1 1.0 CA D:CYS279 4.6 34.1 1.0 N D:ASP415 4.6 38.0 1.0 O D:HOH806 4.9 35.8 1.0 SG D:CYS414 5.0 40.6 0.6 CA D:CYS414 5.0 37.5 0.6 CA D:CYS414 5.0 37.2 0.4 C D:CYS261 5.0 47.8 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 Z54571979


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 Z54571979 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:46.1 occ:1.00 SG D:CYS484 2.3 43.8 1.0 ND1 D:HIS487 2.3 44.0 1.0 SG D:CYS452 2.4 53.9 1.0 SG D:CYS477 2.4 45.2 1.0 CB D:CYS477 3.2 43.1 1.0 CG D:HIS487 3.2 41.7 1.0 CB D:CYS452 3.2 56.7 1.0 CB D:CYS484 3.3 43.6 1.0 CE1 D:HIS487 3.3 44.0 1.0 CB D:HIS487 3.4 39.0 1.0 CA D:CYS452 3.8 57.8 1.0 N D:CYS484 4.0 42.7 1.0 CA D:CYS484 4.2 42.9 1.0 N D:CYS477 4.4 42.3 1.0 N D:HIS487 4.4 40.1 1.0 CA D:CYS477 4.4 42.5 1.0 CD2 D:HIS487 4.4 42.7 1.0 NE2 D:HIS487 4.4 43.8 1.0 CA D:HIS487 4.5 39.5 1.0 N D:CYS452 4.6 56.1 1.0 OG1 D:THR475 4.8 39.5 1.0 CB D:THR475 4.8 39.2 1.0 C D:CYS484 4.9 43.0 1.0 O D:CYS484 4.9 41.8 1.0 O D:HOH792 5.0 41.6 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 Z54571979


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 Z54571979 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:51.9 occ:1.00 ND1 D:HIS229 2.0 54.4 1.0 SG D:CYS210 2.3 55.9 1.0 SG D:CYS207 2.4 51.9 1.0 SG D:CYS226 2.4 47.8 1.0 CE1 D:HIS229 2.7 54.9 1.0 CB D:CYS207 3.0 52.7 1.0 CG D:HIS229 3.2 51.8 1.0 CB D:CYS226 3.4 43.4 1.0 CB D:CYS210 3.4 55.5 1.0 N D:CYS210 3.7 56.2 1.0 CB D:HIS229 3.8 47.7 1.0 N D:CYS226 3.9 42.9 1.0 NE2 D:HIS229 4.0 55.2 1.0 CA D:CYS210 4.0 55.7 1.0 NH1 D:ARG212 4.1 51.5 1.0 CD2 D:HIS229 4.2 53.6 1.0 CA D:CYS226 4.3 42.3 1.0 C D:LEU209 4.5 57.1 1.0 N D:HIS229 4.5 45.7 1.0 CA D:CYS207 4.5 53.7 1.0 C D:CYS210 4.6 55.9 1.0 CD D:ARG212 4.7 50.5 1.0 CB D:LEU209 4.7 58.0 1.0 CB D:ARG212 4.7 49.6 1.0 CA D:HIS229 4.8 46.1 1.0 N D:LEU209 4.9 57.1 1.0 CB D:HIS228 4.9 43.5 1.0 O D:CYS210 4.9 56.2 1.0 CA D:LEU209 4.9 57.4 1.0 CG D:ARG212 4.9 50.2 1.0 C D:CYS226 5.0 40.8 1.0

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