Zinc in PDB 5sm9: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2234920345

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2234920345, PDB code: 5sm9 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)	69.19 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.75, 67.854, 138.385, 90, 90, 90
R / Rfree (%)	23.5 / 27.1

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2234920345 (pdb code 5sm9). 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 Z2234920345, PDB code: 5sm9:
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 Z2234920345


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 Z2234920345 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:35.9 occ:1.00 ND1 D:HIS264 2.0 43.4 1.0 NE2 D:HIS257 2.2 41.0 1.0 SG D:CYS279 2.3 34.4 1.0 SG D:CYS261 2.4 44.5 1.0 CE1 D:HIS264 2.9 44.1 1.0 CD2 D:HIS257 3.0 39.9 1.0 CB D:CYS279 3.1 31.9 1.0 CG D:HIS264 3.1 43.2 1.0 CB D:CYS261 3.1 43.3 1.0 CE1 D:HIS257 3.3 41.1 1.0 CB D:HIS264 3.5 45.7 1.0 NE2 D:HIS264 4.1 44.3 1.0 CG D:HIS257 4.2 39.5 1.0 CD2 D:HIS264 4.2 43.5 1.0 N D:HIS264 4.3 47.9 1.0 ND1 D:HIS257 4.3 41.2 1.0 CA D:HIS264 4.5 47.9 1.0 CA D:CYS261 4.6 43.4 1.0 CA D:CYS279 4.6 32.1 1.0 N D:ASP415 4.6 34.9 1.0 O D:HOH744 4.9 47.3 1.0 SG D:CYS414 5.0 35.7 0.6 C D:CYS261 5.0 44.0 1.0 CA D:CYS414 5.0 34.7 0.6 CA D:CYS414 5.0 34.9 0.4

Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2234920345


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 Z2234920345 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:45.2 occ:1.00 ND1 D:HIS487 2.1 40.7 1.0 SG D:CYS484 2.2 39.0 1.0 SG D:CYS477 2.4 42.0 1.0 SG D:CYS452 2.4 52.0 1.0 CE1 D:HIS487 3.1 40.6 1.0 CG D:HIS487 3.2 39.3 1.0 CB D:CYS477 3.2 38.9 1.0 CB D:CYS452 3.3 54.2 1.0 CB D:CYS484 3.3 40.2 1.0 CB D:HIS487 3.5 39.4 1.0 CA D:CYS452 3.9 55.1 1.0 N D:CYS484 4.0 40.6 1.0 CA D:CYS484 4.2 40.7 1.0 NE2 D:HIS487 4.3 40.7 1.0 CD2 D:HIS487 4.3 39.7 1.0 CA D:CYS477 4.4 38.6 1.0 N D:CYS477 4.4 38.9 1.0 N D:HIS487 4.5 40.8 1.0 CA D:HIS487 4.6 40.3 1.0 N D:CYS452 4.7 53.5 1.0 CB D:THR475 4.7 37.2 1.0 OG1 D:THR475 4.7 37.5 1.0 C D:CYS484 4.9 42.0 1.0 O D:CYS484 4.9 42.2 1.0 O D:HOH859 5.0 35.5 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 Z2234920345


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 Z2234920345 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:49.4 occ:1.00 ND1 D:HIS229 1.9 45.1 1.0 SG D:CYS207 2.3 53.5 1.0 SG D:CYS210 2.4 51.9 1.0 SG D:CYS226 2.6 43.7 1.0 CE1 D:HIS229 2.8 45.6 1.0 CB D:CYS207 3.0 52.6 1.0 CG D:HIS229 3.1 43.6 1.0 CB D:CYS210 3.5 51.8 1.0 CB D:CYS226 3.5 39.6 1.0 CB D:HIS229 3.6 41.6 1.0 N D:CYS210 3.8 51.8 1.0 N D:CYS226 4.0 40.3 1.0 NE2 D:HIS229 4.0 46.2 1.0 CD2 D:HIS229 4.1 45.0 1.0 CA D:CYS210 4.1 51.8 1.0 CA D:CYS226 4.3 39.2 1.0 NH1 D:ARG212 4.4 51.0 1.0 C D:LEU209 4.4 52.5 1.0 N D:HIS229 4.4 40.9 1.0 CA D:CYS207 4.5 52.6 1.0 CB D:LEU209 4.6 52.9 1.0 CA D:HIS229 4.7 41.2 1.0 C D:CYS210 4.7 52.7 1.0 N D:LEU209 4.7 52.8 1.0 CB D:ARG212 4.8 48.1 1.0 CA D:LEU209 4.8 52.7 1.0 CD D:ARG212 4.8 49.6 1.0 CB D:HIS228 4.9 40.5 1.0 O D:CYS210 5.0 53.3 1.0 C D:CYS226 5.0 38.0 1.0

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