Zinc in PDB 5sme: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z437584380

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z437584380, PDB code: 5sme 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)	69.20 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.707, 67.862, 138.4, 90, 90, 90
R / Rfree (%)	21.3 / 25.5

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z437584380 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z437584380 (pdb code 5sme). 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 Z437584380, PDB code: 5sme:
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 Z437584380


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 Z437584380 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:31.0 occ:1.00 ND1 D:HIS264 1.9 29.2 1.0 NE2 D:HIS257 2.0 35.3 1.0 SG D:CYS279 2.2 29.3 1.0 SG D:CYS261 2.4 35.3 1.0 CE1 D:HIS264 2.8 31.6 1.0 CD2 D:HIS257 2.9 34.4 1.0 CG D:HIS264 3.0 31.6 1.0 CB D:CYS279 3.0 28.4 1.0 CB D:CYS261 3.1 35.4 1.0 CE1 D:HIS257 3.1 36.5 1.0 CB D:HIS264 3.4 37.2 1.0 NE2 D:HIS264 3.9 31.6 1.0 CD2 D:HIS264 4.1 29.9 1.0 CG D:HIS257 4.1 35.5 1.0 ND1 D:HIS257 4.1 36.6 1.0 N D:HIS264 4.4 40.4 1.0 CA D:CYS279 4.5 29.5 1.0 CA D:CYS261 4.5 37.2 1.0 N D:ASP415 4.6 32.0 1.0 CA D:HIS264 4.6 40.5 1.0 CA D:CYS414 4.9 32.7 0.6 O D:HOH813 4.9 38.8 1.0 CA D:CYS414 5.0 31.4 0.4 C D:CYS261 5.0 38.9 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 Z437584380


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 Z437584380 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:36.0 occ:1.00 ND1 D:HIS487 2.1 37.2 1.0 SG D:CYS484 2.2 35.7 1.0 SG D:CYS477 2.3 35.0 1.0 SG D:CYS452 2.3 45.3 1.0 CE1 D:HIS487 3.1 36.6 1.0 CB D:CYS452 3.1 51.4 1.0 CG D:HIS487 3.1 35.4 1.0 CB D:CYS477 3.2 35.7 1.0 CB D:CYS484 3.2 37.5 1.0 CB D:HIS487 3.4 35.0 1.0 CA D:CYS452 3.7 54.8 1.0 N D:CYS484 3.9 33.9 1.0 CA D:CYS484 4.1 36.9 1.0 NE2 D:HIS487 4.2 36.8 1.0 CD2 D:HIS487 4.3 35.5 1.0 N D:CYS477 4.3 35.6 1.0 CA D:CYS477 4.3 35.0 1.0 N D:CYS452 4.4 50.3 1.0 N D:HIS487 4.5 36.8 1.0 CA D:HIS487 4.6 35.9 1.0 CB D:THR475 4.7 35.5 1.0 O D:CYS484 4.8 41.3 1.0 C D:CYS484 4.8 41.6 1.0 OG1 D:THR475 4.8 33.8 1.0 C D:CYS452 5.0 56.0 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 Z437584380


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 Z437584380 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:42.2 occ:1.00 ND1 D:HIS229 1.8 39.2 1.0 SG D:CYS207 2.3 43.1 1.0 SG D:CYS210 2.3 40.4 1.0 SG D:CYS226 2.5 41.4 1.0 CE1 D:HIS229 2.7 40.3 1.0 CG D:HIS229 2.9 37.9 1.0 CB D:CYS207 3.0 42.5 1.0 CB D:CYS210 3.4 44.5 1.0 CB D:HIS229 3.4 38.3 1.0 CB D:CYS226 3.5 40.1 1.0 N D:CYS210 3.8 46.6 1.0 NE2 D:HIS229 3.9 37.8 1.0 N D:CYS226 4.0 39.8 1.0 CD2 D:HIS229 4.0 37.2 1.0 CA D:CYS210 4.1 41.8 1.0 NH1 D:ARG212 4.2 50.5 1.0 CA D:CYS226 4.3 37.4 1.0 C D:LEU209 4.4 49.2 1.0 CA D:CYS207 4.4 46.0 1.0 N D:HIS229 4.6 40.2 1.0 CA D:HIS229 4.6 38.7 1.0 C D:CYS210 4.7 43.2 1.0 CB D:LEU209 4.7 47.8 1.0 CB D:ARG212 4.8 46.1 1.0 CB D:HIS228 4.8 38.5 1.0 N D:LEU209 4.9 50.4 1.0 CA D:LEU209 4.9 49.4 1.0 CD D:ARG212 4.9 42.4 1.0 O D:LEU209 4.9 53.6 1.0 O D:CYS210 4.9 47.2 1.0 C D:CYS226 5.0 38.5 1.0

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