Zinc in PDB 5sm8: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2027158783

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2027158783, PDB code: 5sm8 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)	69.26 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.586, 68.023, 138.519, 90, 90, 90
R / Rfree (%)	22.4 / 26.7

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2027158783 (pdb code 5sm8). 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 Z2027158783, PDB code: 5sm8:
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 Z2027158783


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 Z2027158783 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:37.0 occ:1.00 ND1 D:HIS264 1.9 38.3 1.0 NE2 D:HIS257 2.1 47.9 1.0 SG D:CYS279 2.2 30.1 1.0 SG D:CYS261 2.4 41.4 1.0 CE1 D:HIS264 2.7 41.0 1.0 CD2 D:HIS257 3.0 42.9 1.0 CG D:HIS264 3.0 39.9 1.0 CB D:CYS279 3.0 32.4 1.0 CB D:CYS261 3.1 41.2 1.0 CE1 D:HIS257 3.2 46.4 1.0 CB D:HIS264 3.5 44.2 1.0 NE2 D:HIS264 3.9 40.2 1.0 CD2 D:HIS264 4.1 36.8 1.0 CG D:HIS257 4.1 46.9 1.0 ND1 D:HIS257 4.2 45.2 1.0 N D:HIS264 4.4 42.9 1.0 CA D:CYS279 4.5 32.0 1.0 CA D:CYS261 4.6 40.0 1.0 CA D:HIS264 4.6 45.6 1.0 N D:ASP415 4.6 35.1 1.0 C D:CYS261 4.9 42.7 1.0 SG D:CYS414 5.0 39.0 0.6 O D:CYS261 5.0 44.8 1.0 CA D:CYS414 5.0 36.5 0.4 CA D:CYS414 5.0 35.5 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 Z2027158783


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 Z2027158783 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:41.7 occ:1.00 SG D:CYS484 2.2 39.4 1.0 ND1 D:HIS487 2.2 36.5 1.0 SG D:CYS452 2.3 50.5 1.0 SG D:CYS477 2.3 43.1 1.0 CB D:CYS452 3.0 56.0 1.0 CB D:CYS477 3.1 39.8 1.0 CE1 D:HIS487 3.2 36.7 1.0 CG D:HIS487 3.2 32.5 1.0 CB D:CYS484 3.3 37.6 1.0 CB D:HIS487 3.5 33.8 1.0 CA D:CYS452 3.7 62.5 1.0 N D:CYS484 3.9 33.7 1.0 CA D:CYS484 4.1 35.0 1.0 N D:CYS477 4.2 41.6 1.0 CA D:CYS477 4.3 39.5 1.0 NE2 D:HIS487 4.3 39.6 1.0 CD2 D:HIS487 4.4 35.4 1.0 N D:CYS452 4.4 58.0 1.0 N D:HIS487 4.5 38.4 1.0 CA D:HIS487 4.6 37.7 1.0 CB D:THR475 4.7 44.0 1.0 O D:CYS484 4.8 43.1 1.0 C D:CYS484 4.8 41.1 1.0 O D:HOH901 4.9 34.5 1.0 OG1 D:THR475 4.9 40.4 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 Z2027158783


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 Z2027158783 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:47.3 occ:1.00 ND1 D:HIS229 1.9 45.4 1.0 SG D:CYS210 2.3 45.6 1.0 SG D:CYS207 2.3 47.9 1.0 SG D:CYS226 2.5 47.2 1.0 CE1 D:HIS229 2.7 46.2 1.0 CB D:CYS207 3.0 44.7 1.0 CG D:HIS229 3.0 44.5 1.0 CB D:CYS210 3.4 48.7 1.0 CB D:HIS229 3.5 43.3 1.0 CB D:CYS226 3.6 43.0 1.0 N D:CYS210 3.9 53.2 1.0 NE2 D:HIS229 3.9 44.3 1.0 N D:CYS226 4.0 41.7 1.0 CD2 D:HIS229 4.1 43.9 1.0 NH1 D:ARG212 4.1 59.4 1.0 CA D:CYS210 4.1 45.9 1.0 C D:LEU209 4.3 50.5 1.0 CA D:CYS226 4.3 39.8 1.0 CA D:CYS207 4.4 47.2 1.0 N D:HIS229 4.5 44.7 1.0 CB D:LEU209 4.7 50.9 1.0 CA D:HIS229 4.7 42.3 1.0 C D:CYS210 4.7 48.5 1.0 CB D:ARG212 4.7 55.8 1.0 O D:LEU209 4.7 60.4 1.0 N D:LEU209 4.8 56.8 1.0 CA D:LEU209 4.8 50.1 1.0 CB D:HIS228 4.8 43.7 1.0 C D:CYS226 5.0 39.1 1.0

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