Zinc in PDB 5smi: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z71580604

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z71580604, PDB code: 5smi 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)	69.33 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.682, 68.341, 138.651, 90, 90, 90
R / Rfree (%)	26.8 / 32.9

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z71580604 (pdb code 5smi). 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 Z71580604, PDB code: 5smi:
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 Z71580604


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 Z71580604 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:34.5 occ:1.00 ND1 D:HIS264 1.9 32.0 1.0 NE2 D:HIS257 2.1 39.3 1.0 SG D:CYS279 2.2 29.9 1.0 SG D:CYS261 2.3 40.8 1.0 CE1 D:HIS264 2.6 35.4 1.0 CD2 D:HIS257 3.0 38.3 1.0 CB D:CYS279 3.0 30.7 1.0 CG D:HIS264 3.1 33.2 1.0 CE1 D:HIS257 3.1 37.2 1.0 CB D:CYS261 3.2 39.9 1.0 CB D:HIS264 3.6 41.6 1.0 NE2 D:HIS264 3.8 33.9 1.0 CD2 D:HIS264 4.0 31.0 1.0 CG D:HIS257 4.1 42.4 1.0 ND1 D:HIS257 4.2 39.5 1.0 N D:HIS264 4.4 41.7 1.0 CA D:CYS279 4.5 30.7 1.0 N D:ASP415 4.6 30.1 1.0 CA D:CYS261 4.6 38.3 1.0 CA D:HIS264 4.6 41.5 1.0 CA D:CYS414 4.9 31.6 0.4 CA D:CYS414 4.9 34.1 0.6 SG D:CYS414 5.0 42.2 0.6 O D:HOH788 5.0 40.9 1.0 O D:CYS261 5.0 37.6 1.0 CA D:MET276 5.0 32.5 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 Z71580604


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 Z71580604 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:39.3 occ:1.00 ND1 D:HIS487 2.2 31.6 1.0 SG D:CYS484 2.3 39.0 1.0 SG D:CYS452 2.3 48.1 1.0 SG D:CYS477 2.3 36.0 1.0 CB D:CYS452 3.1 49.3 1.0 CB D:CYS477 3.1 36.8 1.0 CE1 D:HIS487 3.1 29.2 1.0 CG D:HIS487 3.2 31.3 1.0 CB D:CYS484 3.2 38.5 1.0 CB D:HIS487 3.5 32.5 1.0 CA D:CYS452 3.8 55.2 1.0 N D:CYS484 3.9 33.7 1.0 CA D:CYS484 4.1 37.7 1.0 NE2 D:HIS487 4.3 31.0 1.0 N D:CYS477 4.3 41.2 1.0 CA D:CYS477 4.3 38.6 1.0 CD2 D:HIS487 4.3 33.7 1.0 N D:HIS487 4.5 37.5 1.0 N D:CYS452 4.5 54.3 1.0 CA D:HIS487 4.6 35.7 1.0 C D:CYS484 4.7 39.1 1.0 OG1 D:THR475 4.7 39.0 1.0 CB D:THR475 4.8 41.0 1.0 O D:CYS484 4.8 44.3 1.0 O D:HOH939 4.9 39.4 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 Z71580604


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 Z71580604 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:45.5 occ:1.00 ND1 D:HIS229 1.9 39.2 1.0 SG D:CYS210 2.2 42.3 1.0 SG D:CYS207 2.3 46.1 1.0 SG D:CYS226 2.5 43.6 1.0 CE1 D:HIS229 2.8 36.5 1.0 CG D:HIS229 3.0 36.9 1.0 CB D:CYS207 3.0 42.1 1.0 CB D:HIS229 3.4 37.0 1.0 CB D:CYS210 3.5 43.3 1.0 CB D:CYS226 3.5 39.8 1.0 NH1 D:ARG212 3.9 61.1 1.0 NE2 D:HIS229 3.9 38.9 1.0 N D:CYS210 4.0 44.4 1.0 N D:CYS226 4.0 39.1 1.0 CD2 D:HIS229 4.1 36.5 1.0 CA D:CYS210 4.2 41.3 1.0 C D:LEU209 4.3 45.5 1.0 CA D:CYS226 4.4 37.7 1.0 N D:HIS229 4.4 44.0 1.0 CA D:CYS207 4.5 44.0 1.0 CB D:ARG212 4.5 49.5 1.0 CA D:HIS229 4.6 38.3 1.0 CB D:LEU209 4.6 45.9 1.0 N D:LEU209 4.7 52.6 1.0 C D:CYS210 4.8 41.1 1.0 CB D:HIS228 4.8 39.9 1.0 O D:LEU209 4.8 53.7 1.0 CA D:LEU209 4.8 44.9 1.0 O D:CYS210 4.8 46.5 1.0 CD D:ARG212 4.9 50.5 1.0 CG D:ARG212 4.9 48.3 1.0 C D:CYS226 4.9 38.3 1.0

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