Zinc in PDB 5slo: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56983806

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56983806, PDB code: 5slo 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)	69.24 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.561, 67.79, 138.482, 90, 90, 90
R / Rfree (%)	24.3 / 28.1

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56983806 (pdb code 5slo). 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 Z56983806, PDB code: 5slo:
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 Z56983806


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 Z56983806 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:37.3 occ:1.00 ND1 D:HIS264 2.0 46.6 1.0 NE2 D:HIS257 2.1 43.3 1.0 SG D:CYS279 2.3 34.1 1.0 SG D:CYS261 2.4 40.7 1.0 CE1 D:HIS264 2.9 46.8 1.0 CD2 D:HIS257 3.0 41.7 1.0 CG D:HIS264 3.1 46.0 1.0 CB D:CYS261 3.1 44.1 1.0 CB D:CYS279 3.1 31.4 1.0 CE1 D:HIS257 3.2 43.1 1.0 CB D:HIS264 3.5 47.2 1.0 NE2 D:HIS264 4.0 46.7 1.0 CG D:HIS257 4.2 41.0 1.0 CD2 D:HIS264 4.2 45.9 1.0 N D:HIS264 4.3 48.2 1.0 ND1 D:HIS257 4.3 42.5 1.0 CA D:HIS264 4.5 49.1 1.0 CA D:CYS261 4.6 45.4 1.0 CA D:CYS279 4.6 31.8 1.0 N D:ASP415 4.6 35.4 1.0 O D:HOH735 4.9 34.7 1.0 C D:CYS261 5.0 46.2 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 Z56983806


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 Z56983806 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:42.1 occ:1.00 ND1 D:HIS487 2.1 39.5 1.0 SG D:CYS484 2.3 39.5 1.0 SG D:CYS452 2.4 50.9 1.0 SG D:CYS477 2.4 42.3 1.0 CE1 D:HIS487 3.1 39.7 1.0 CG D:HIS487 3.2 37.2 1.0 CB D:CYS477 3.2 38.9 1.0 CB D:CYS452 3.2 54.9 1.0 CB D:CYS484 3.3 39.7 1.0 CB D:HIS487 3.5 35.5 1.0 CA D:CYS452 3.8 56.7 1.0 N D:CYS484 3.9 40.0 1.0 CA D:CYS484 4.2 39.6 1.0 NE2 D:HIS487 4.3 39.9 1.0 CD2 D:HIS487 4.3 38.6 1.0 N D:CYS477 4.3 38.7 1.0 CA D:CYS477 4.4 38.6 1.0 N D:HIS487 4.4 36.3 1.0 CA D:HIS487 4.5 36.0 1.0 N D:CYS452 4.6 55.1 1.0 OG1 D:THR475 4.8 37.6 1.0 CB D:THR475 4.8 36.6 1.0 C D:CYS484 4.8 40.3 1.0 O D:CYS484 4.9 40.0 1.0 C D:CYS452 5.0 60.4 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 Z56983806


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 Z56983806 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:48.6 occ:1.00 ND1 D:HIS229 2.0 48.1 1.0 SG D:CYS207 2.3 52.2 1.0 SG D:CYS210 2.4 53.9 1.0 SG D:CYS226 2.5 46.0 1.0 CE1 D:HIS229 2.8 48.6 1.0 CB D:CYS207 3.0 52.6 1.0 CG D:HIS229 3.1 46.1 1.0 CB D:CYS210 3.4 53.2 1.0 CB D:CYS226 3.5 40.2 1.0 CB D:HIS229 3.7 43.0 1.0 N D:CYS210 3.8 53.8 1.0 N D:CYS226 4.0 39.8 1.0 NE2 D:HIS229 4.0 49.2 1.0 CA D:CYS210 4.1 53.3 1.0 CD2 D:HIS229 4.2 48.1 1.0 NH1 D:ARG212 4.2 49.7 1.0 CA D:CYS226 4.4 39.3 1.0 C D:LEU209 4.4 54.8 1.0 N D:HIS229 4.5 41.4 1.0 CA D:CYS207 4.5 53.3 1.0 C D:CYS210 4.7 53.3 1.0 CB D:LEU209 4.7 55.7 1.0 CA D:HIS229 4.7 42.0 1.0 CB D:ARG212 4.7 47.0 1.0 N D:LEU209 4.8 55.2 1.0 CA D:LEU209 4.8 55.2 1.0 CD D:ARG212 4.9 48.1 1.0 O D:CYS210 4.9 54.2 1.0 CB D:HIS228 5.0 41.0 1.0 O D:LEU209 5.0 55.3 1.0

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