Zinc in PDB 5sm2: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474, PDB code: 5sm2 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 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.646, 67.43, 138.52, 90, 90, 90
R / Rfree (%)	25 / 27

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 (pdb code 5sm2). 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 Z3006151474, PDB code: 5sm2:
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 Z3006151474


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 Z3006151474 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:38.0 occ:1.00 ND1 D:HIS264 1.9 43.1 1.0 NE2 D:HIS257 2.2 44.1 1.0 SG D:CYS279 2.3 36.9 1.0 SG D:CYS261 2.4 41.9 1.0 CE1 D:HIS264 2.8 43.4 1.0 CD2 D:HIS257 3.0 42.7 1.0 CG D:HIS264 3.1 42.9 1.0 CB D:CYS261 3.1 44.0 1.0 CB D:CYS279 3.1 33.0 1.0 CE1 D:HIS257 3.3 43.9 1.0 CB D:HIS264 3.6 45.2 1.0 NE2 D:HIS264 4.0 43.5 1.0 CD2 D:HIS264 4.2 43.0 1.0 CG D:HIS257 4.2 42.2 1.0 N D:HIS264 4.3 47.6 1.0 ND1 D:HIS257 4.4 43.4 1.0 CA D:CYS261 4.6 45.0 1.0 CA D:HIS264 4.6 47.9 1.0 N D:ASP415 4.6 36.7 1.0 CA D:CYS279 4.6 33.0 1.0 O D:HOH804 4.9 35.1 1.0 CA D:CYS414 5.0 35.9 0.4 SG D:CYS414 5.0 37.8 0.6 CA D:CYS414 5.0 35.8 0.6 C D:CYS261 5.0 45.5 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 Z3006151474


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 Z3006151474 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:43.8 occ:1.00 ND1 D:HIS487 2.2 42.0 1.0 SG D:CYS484 2.3 41.2 1.0 SG D:CYS452 2.4 52.4 1.0 SG D:CYS477 2.4 40.9 1.0 CG D:HIS487 3.1 39.4 1.0 CB D:CYS477 3.2 39.4 1.0 CE1 D:HIS487 3.2 41.9 1.0 CB D:CYS452 3.2 56.2 1.0 CB D:CYS484 3.3 41.2 1.0 CB D:HIS487 3.4 36.6 1.0 CA D:CYS452 3.8 58.1 1.0 N D:CYS484 3.9 40.5 1.0 CA D:CYS484 4.2 40.9 1.0 CD2 D:HIS487 4.3 40.6 1.0 N D:CYS477 4.3 40.5 1.0 NE2 D:HIS487 4.4 41.6 1.0 CA D:CYS477 4.4 39.6 1.0 N D:HIS487 4.4 37.0 1.0 CA D:HIS487 4.5 36.8 1.0 OG1 D:THR475 4.6 39.5 1.0 N D:CYS452 4.7 56.8 1.0 CB D:THR475 4.7 39.1 1.0 C D:CYS484 4.8 41.4 1.0 O D:CYS484 4.8 41.1 1.0 C D:CYS452 5.0 61.4 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 Z3006151474


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 Z3006151474 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:48.1 occ:1.00 ND1 D:HIS229 2.1 50.6 1.0 SG D:CYS207 2.3 51.5 1.0 SG D:CYS210 2.4 53.4 1.0 SG D:CYS226 2.4 45.4 1.0 CE1 D:HIS229 2.9 50.7 1.0 CB D:CYS207 3.0 51.4 1.0 CG D:HIS229 3.2 48.3 1.0 CB D:CYS226 3.4 41.8 1.0 CB D:CYS210 3.5 52.9 1.0 CB D:HIS229 3.7 44.7 1.0 N D:CYS210 3.8 53.3 1.0 N D:CYS226 4.0 41.1 1.0 NE2 D:HIS229 4.1 51.0 1.0 CA D:CYS210 4.1 52.8 1.0 NH1 D:ARG212 4.3 47.6 1.0 CD2 D:HIS229 4.3 49.7 1.0 CA D:CYS226 4.3 40.9 1.0 C D:LEU209 4.4 54.5 1.0 N D:HIS229 4.5 42.8 1.0 CA D:CYS207 4.5 52.3 1.0 CB D:LEU209 4.7 55.5 1.0 CD D:ARG212 4.7 47.8 1.0 C D:CYS210 4.7 53.0 1.0 CB D:ARG212 4.7 47.4 1.0 CA D:HIS229 4.8 43.3 1.0 N D:LEU209 4.8 55.0 1.0 CA D:LEU209 4.8 55.0 1.0 CB D:HIS228 4.9 41.1 1.0 C D:CYS226 5.0 39.7 1.0

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