Zinc in PDB 5sky: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z466628048

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z466628048, PDB code: 5sky 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)	60.90 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.85, 68.59, 138.13, 90, 90, 90
R / Rfree (%)	21.3 / 24.8

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z466628048 (pdb code 5sky). 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 Z466628048, PDB code: 5sky:
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 Z466628048


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 Z466628048 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:38.7 occ:1.00 ND1 D:HIS264 2.0 43.1 1.0 NE2 D:HIS257 2.2 43.1 1.0 SG D:CYS279 2.3 36.4 1.0 SG D:CYS261 2.4 42.8 1.0 CE1 D:HIS264 2.8 43.4 1.0 CD2 D:HIS257 3.0 42.5 1.0 CB D:CYS261 3.1 43.1 1.0 CB D:CYS279 3.1 36.2 1.0 CG D:HIS264 3.2 42.7 1.0 CE1 D:HIS257 3.2 43.2 1.0 CB D:HIS264 3.7 45.5 1.0 NE2 D:HIS264 4.0 43.1 1.0 CG D:HIS257 4.2 42.0 1.0 CD2 D:HIS264 4.2 42.4 1.0 ND1 D:HIS257 4.3 42.9 1.0 N D:HIS264 4.4 47.1 1.0 CA D:CYS261 4.5 44.4 1.0 CA D:CYS279 4.6 36.0 1.0 N D:ASP415 4.6 36.9 1.0 CA D:HIS264 4.7 47.6 1.0 O D:HOH796 4.9 42.8 1.0 SG D:CYS414 4.9 44.2 0.6 CA D:CYS414 4.9 36.8 0.4 C D:CYS261 4.9 45.1 1.0 CA D:CYS414 5.0 37.4 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 Z466628048


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 Z466628048 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:43.5 occ:1.00 ND1 D:HIS487 2.2 40.4 1.0 SG D:CYS484 2.3 39.5 1.0 SG D:CYS452 2.4 51.6 1.0 SG D:CYS477 2.4 42.7 1.0 CE1 D:HIS487 3.1 40.4 1.0 CB D:CYS452 3.2 52.5 1.0 CB D:CYS477 3.2 39.2 1.0 CG D:HIS487 3.2 39.1 1.0 CB D:CYS484 3.4 40.8 1.0 CB D:HIS487 3.6 38.3 1.0 CA D:CYS452 3.7 53.1 1.0 N D:CYS484 4.0 41.9 1.0 CA D:CYS484 4.3 41.4 1.0 NE2 D:HIS487 4.3 40.4 1.0 CD2 D:HIS487 4.4 39.4 1.0 N D:CYS477 4.4 39.7 1.0 CA D:CYS477 4.4 39.5 1.0 N D:CYS452 4.5 51.6 1.0 N D:HIS487 4.5 38.3 1.0 CA D:HIS487 4.7 38.7 1.0 CB D:THR475 4.7 38.1 1.0 OG1 D:THR475 4.7 38.3 1.0 O D:HOH831 4.9 40.1 1.0 C D:CYS484 5.0 41.9 1.0 O D:CYS484 5.0 42.7 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 Z466628048


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 Z466628048 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:49.0 occ:1.00 ND1 D:HIS229 1.9 47.9 1.0 SG D:CYS207 2.2 50.0 1.0 SG D:CYS210 2.3 54.7 1.0 SG D:CYS226 2.5 46.6 1.0 CE1 D:HIS229 2.7 48.5 1.0 CB D:CYS207 3.0 49.9 1.0 CG D:HIS229 3.1 45.5 1.0 CB D:CYS210 3.3 51.4 1.0 CB D:CYS226 3.5 43.0 1.0 CB D:HIS229 3.7 41.9 1.0 N D:CYS210 3.7 50.6 1.0 NE2 D:HIS229 3.9 47.8 1.0 CA D:CYS210 4.0 50.5 1.0 N D:CYS226 4.0 42.2 1.0 CD2 D:HIS229 4.2 46.6 1.0 NH1 D:ARG212 4.2 44.6 1.0 C D:LEU209 4.3 51.5 1.0 CA D:CYS226 4.3 41.8 1.0 N D:HIS229 4.4 41.0 1.0 CA D:CYS207 4.5 50.0 1.0 C D:CYS210 4.5 50.4 1.0 CD D:ARG212 4.7 47.2 1.0 CA D:HIS229 4.7 41.1 1.0 CB D:LEU209 4.7 51.9 1.0 N D:LEU209 4.7 51.8 1.0 CB D:ARG212 4.8 46.5 1.0 CA D:LEU209 4.8 51.7 1.0 O D:CYS210 4.8 50.5 1.0 CB D:HIS228 4.9 40.5 1.0 O D:LEU209 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.