Zinc in PDB 5skx: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z126932614

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z126932614, PDB code: 5skx 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)	69.27 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.652, 67.696, 138.531, 90, 90, 90
R / Rfree (%)	18.3 / 27.5

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z126932614 (pdb code 5skx). 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 Z126932614, PDB code: 5skx:
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 Z126932614


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 Z126932614 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn604 b:30.2 occ:1.00 ND1 D:HIS264 1.9 48.5 1.0 NE2 D:HIS257 2.1 37.1 1.0 SG D:CYS261 2.3 46.9 1.0 SG D:CYS279 2.3 23.9 1.0 CE1 D:HIS264 2.8 49.1 1.0 CG D:HIS264 3.0 47.2 1.0 CD2 D:HIS257 3.0 36.7 1.0 CB D:CYS261 3.1 44.7 1.0 CE1 D:HIS257 3.2 37.4 1.0 CB D:CYS279 3.3 26.0 1.0 CB D:HIS264 3.4 47.0 1.0 NE2 D:HIS264 4.0 49.2 1.0 CD2 D:HIS264 4.1 48.2 1.0 N D:HIS264 4.2 47.3 1.0 CG D:HIS257 4.2 36.5 1.0 ND1 D:HIS257 4.3 37.9 1.0 CA D:HIS264 4.4 47.8 1.0 CA D:CYS261 4.5 44.6 1.0 N D:ASP415 4.6 26.9 1.0 CA D:CYS279 4.7 27.4 1.0 O D:HOH751 4.8 29.7 1.0 CA D:CYS414 4.9 26.1 0.4 C D:CYS261 4.9 45.7 1.0 CA D:CYS414 5.0 27.2 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 Z126932614


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 Z126932614 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn605 b:37.8 occ:1.00 SG D:CYS484 2.2 39.2 1.0 SG D:CYS477 2.3 41.1 1.0 ND1 D:HIS487 2.5 40.0 1.0 SG D:CYS452 2.6 56.1 1.0 CB D:CYS452 3.2 54.7 1.0 CB D:CYS477 3.3 36.8 1.0 CE1 D:HIS487 3.4 40.4 1.0 CG D:HIS487 3.4 38.3 1.0 CB D:CYS484 3.4 39.2 1.0 CB D:HIS487 3.7 37.0 1.0 CA D:CYS452 3.9 54.9 1.0 N D:CYS484 4.0 39.4 1.0 N D:CYS477 4.3 36.4 1.0 CA D:CYS484 4.3 39.5 1.0 CA D:CYS477 4.4 36.2 1.0 NE2 D:HIS487 4.5 40.5 1.0 CD2 D:HIS487 4.5 39.4 1.0 CB D:THR475 4.6 35.8 1.0 N D:CYS452 4.7 53.4 1.0 N D:HIS487 4.7 37.3 1.0 OG1 D:THR475 4.7 36.5 1.0 CA D:HIS487 4.8 36.8 1.0 O D:HOH823 4.9 28.8 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 Z126932614


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 Z126932614 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn606 b:39.1 occ:1.00 ND1 D:HIS229 2.0 42.8 1.0 SG D:CYS207 2.2 45.0 1.0 SG D:CYS210 2.4 46.3 1.0 SG D:CYS226 2.7 45.1 1.0 CE1 D:HIS229 2.9 43.6 1.0 CB D:CYS207 3.0 44.0 1.0 CG D:HIS229 3.2 40.6 1.0 CB D:CYS210 3.3 44.8 1.0 CB D:CYS226 3.4 39.9 1.0 CB D:HIS229 3.6 37.7 1.0 N D:CYS226 3.8 39.5 1.0 N D:CYS210 3.9 45.1 1.0 NE2 D:HIS229 4.1 43.2 1.0 CA D:CYS210 4.1 44.8 1.0 NH1 D:ARG212 4.2 55.9 1.0 CA D:CYS226 4.2 38.8 1.0 CD2 D:HIS229 4.2 41.9 1.0 N D:HIS229 4.3 36.2 1.0 CA D:CYS207 4.5 44.4 1.0 C D:LEU209 4.5 45.6 1.0 CA D:HIS229 4.6 36.6 1.0 C D:CYS210 4.7 44.7 1.0 CB D:LEU209 4.8 46.6 1.0 C D:CYS226 4.8 38.1 1.0 CB D:ARG212 4.9 41.4 1.0 N D:LEU209 4.9 45.4 1.0 CA D:LEU209 5.0 45.9 1.0 C D:ALA225 5.0 41.0 1.0

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