Zinc in PDB 5skz: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57258487

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57258487, PDB code: 5skz 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 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.681, 68.153, 138.486, 90, 90, 90
R / Rfree (%)	21.5 / 24.4

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57258487 (pdb code 5skz). 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 Z57258487, PDB code: 5skz:
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 Z57258487


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 Z57258487 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:32.9 occ:1.00 ND1 D:HIS264 2.0 37.3 1.0 NE2 D:HIS257 2.1 35.4 1.0 SG D:CYS279 2.3 32.1 1.0 SG D:CYS261 2.4 36.8 1.0 CE1 D:HIS264 2.9 38.0 1.0 CD2 D:HIS257 3.0 35.1 1.0 CG D:HIS264 3.1 37.5 1.0 CB D:CYS279 3.1 28.8 1.0 CB D:CYS261 3.1 37.4 1.0 CE1 D:HIS257 3.2 35.4 1.0 CB D:HIS264 3.5 40.6 1.0 NE2 D:HIS264 4.1 37.9 1.0 CD2 D:HIS264 4.2 37.1 1.0 CG D:HIS257 4.2 34.9 1.0 ND1 D:HIS257 4.3 35.9 1.0 N D:HIS264 4.3 42.4 1.0 CA D:HIS264 4.6 43.0 1.0 N D:ASP415 4.6 32.9 1.0 CA D:CYS279 4.6 29.0 1.0 CA D:CYS261 4.6 38.8 1.0 SG D:CYS414 4.9 33.9 0.6 O D:HOH848 4.9 34.3 1.0 CA D:CYS414 5.0 32.2 0.6 C D:CYS261 5.0 39.1 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 Z57258487


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 Z57258487 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:38.5 occ:1.00 ND1 D:HIS487 2.1 36.4 1.0 SG D:CYS484 2.3 37.0 1.0 SG D:CYS452 2.3 44.3 1.0 SG D:CYS477 2.3 37.0 1.0 CE1 D:HIS487 3.1 36.3 1.0 CG D:HIS487 3.1 35.1 1.0 CB D:CYS477 3.2 35.1 1.0 CB D:CYS452 3.2 49.0 1.0 CB D:CYS484 3.3 36.8 1.0 CB D:HIS487 3.5 33.7 1.0 CA D:CYS452 3.7 50.9 1.0 N D:CYS484 4.0 37.0 1.0 NE2 D:HIS487 4.2 36.4 1.0 CA D:CYS484 4.2 36.9 1.0 CD2 D:HIS487 4.3 35.7 1.0 N D:CYS477 4.4 35.9 1.0 CA D:CYS477 4.4 35.3 1.0 N D:HIS487 4.4 34.3 1.0 N D:CYS452 4.5 49.3 1.0 CA D:HIS487 4.6 33.8 1.0 OG1 D:THR475 4.7 36.1 1.0 CB D:THR475 4.7 35.3 1.0 O D:CYS484 4.9 37.4 1.0 C D:CYS484 4.9 37.5 1.0 C D:CYS452 5.0 54.5 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 Z57258487


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 Z57258487 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:44.7 occ:1.00 ND1 D:HIS229 1.9 45.9 1.0 SG D:CYS207 2.3 47.8 1.0 SG D:CYS210 2.4 50.7 1.0 SG D:CYS226 2.4 42.5 1.0 CE1 D:HIS229 2.8 46.3 1.0 CG D:HIS229 3.1 43.6 1.0 CB D:CYS207 3.1 48.0 1.0 CB D:CYS210 3.4 50.1 1.0 CB D:CYS226 3.5 38.3 1.0 CB D:HIS229 3.6 40.6 1.0 N D:CYS210 3.8 50.5 1.0 N D:CYS226 4.0 37.5 1.0 NE2 D:HIS229 4.0 46.3 1.0 CA D:CYS210 4.1 50.1 1.0 CD2 D:HIS229 4.2 45.0 1.0 NH1 D:ARG212 4.2 47.9 1.0 CA D:CYS226 4.3 37.1 1.0 N D:HIS229 4.4 38.6 1.0 C D:LEU209 4.4 51.5 1.0 CA D:CYS207 4.6 48.6 1.0 CA D:HIS229 4.6 39.2 1.0 CB D:LEU209 4.7 51.5 1.0 C D:CYS210 4.7 50.3 1.0 N D:LEU209 4.8 51.5 1.0 CD D:ARG212 4.8 45.2 1.0 CB D:ARG212 4.8 44.9 1.0 CA D:LEU209 4.8 51.4 1.0 CB D:HIS228 4.9 38.0 1.0 O D:CYS210 4.9 50.9 1.0 C D:CYS226 5.0 35.7 1.0 O D:LEU209 5.0 52.2 1.0

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