Zinc in PDB 5slp: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z373768898

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z373768898, PDB code: 5slp 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)	34.63 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.734, 68.096, 138.516, 90, 90, 90
R / Rfree (%)	23 / 26

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z373768898 (pdb code 5slp). 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 Z373768898, PDB code: 5slp:
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 Z373768898


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 Z373768898 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:33.4 occ:1.00 ND1 D:HIS264 2.0 40.5 1.0 NE2 D:HIS257 2.1 38.0 1.0 SG D:CYS279 2.2 32.0 1.0 SG D:CYS261 2.4 37.1 1.0 CE1 D:HIS264 2.9 41.0 1.0 CD2 D:HIS257 3.0 36.5 1.0 CG D:HIS264 3.1 40.5 1.0 CB D:CYS279 3.1 29.2 1.0 CB D:CYS261 3.1 39.3 1.0 CE1 D:HIS257 3.2 38.3 1.0 CB D:HIS264 3.5 42.7 1.0 NE2 D:HIS264 4.1 41.3 1.0 CD2 D:HIS264 4.2 40.6 1.0 CG D:HIS257 4.2 36.8 1.0 ND1 D:HIS257 4.2 38.4 1.0 N D:HIS264 4.3 44.4 1.0 CA D:HIS264 4.6 45.0 1.0 CA D:CYS279 4.6 29.3 1.0 N D:ASP415 4.6 32.9 1.0 CA D:CYS261 4.6 41.0 1.0 SG D:CYS414 4.9 35.1 0.6 O D:HOH806 4.9 32.5 1.0 CA D:CYS414 5.0 33.1 0.6 CA D:CYS414 5.0 32.8 0.4 C D:CYS261 5.0 42.2 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 Z373768898


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 Z373768898 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:37.9 occ:1.00 ND1 D:HIS487 2.1 36.7 1.0 SG D:CYS484 2.3 35.8 1.0 SG D:CYS452 2.3 41.7 1.0 SG D:CYS477 2.4 36.7 1.0 CE1 D:HIS487 3.1 36.5 1.0 CG D:HIS487 3.2 34.7 1.0 CB D:CYS452 3.2 45.4 1.0 CB D:CYS477 3.2 34.4 1.0 CB D:CYS484 3.3 34.8 1.0 CB D:HIS487 3.5 32.1 1.0 CA D:CYS452 3.8 46.9 1.0 N D:CYS484 4.1 34.1 1.0 CA D:CYS484 4.3 34.4 1.0 NE2 D:HIS487 4.3 36.7 1.0 CD2 D:HIS487 4.3 35.8 1.0 N D:CYS477 4.3 35.0 1.0 CA D:CYS477 4.4 34.7 1.0 N D:HIS487 4.5 32.8 1.0 CA D:HIS487 4.6 32.3 1.0 N D:CYS452 4.6 45.7 1.0 OG1 D:THR475 4.7 32.8 1.0 CB D:THR475 4.7 32.5 1.0 C D:CYS484 4.9 35.0 1.0 O D:CYS484 4.9 34.6 1.0 C D:CYS452 5.0 49.8 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 Z373768898


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 Z373768898 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:43.5 occ:1.00 ND1 D:HIS229 2.0 44.1 1.0 SG D:CYS210 2.3 47.9 1.0 SG D:CYS207 2.3 46.2 1.0 SG D:CYS226 2.5 40.6 1.0 CE1 D:HIS229 2.8 44.4 1.0 CB D:CYS207 3.0 45.7 1.0 CG D:HIS229 3.2 42.0 1.0 CB D:CYS210 3.5 47.8 1.0 CB D:CYS226 3.5 35.2 1.0 CB D:HIS229 3.8 39.0 1.0 N D:CYS210 3.8 48.4 1.0 N D:CYS226 4.0 34.6 1.0 NE2 D:HIS229 4.1 44.6 1.0 CA D:CYS210 4.1 48.1 1.0 NH1 D:ARG212 4.2 42.8 1.0 CD2 D:HIS229 4.3 43.3 1.0 CA D:CYS226 4.3 34.3 1.0 C D:LEU209 4.4 49.5 1.0 N D:HIS229 4.5 37.4 1.0 CA D:CYS207 4.5 46.2 1.0 CB D:LEU209 4.7 50.0 1.0 C D:CYS210 4.7 48.6 1.0 N D:LEU209 4.8 49.2 1.0 CB D:ARG212 4.8 42.2 1.0 CD D:ARG212 4.8 42.3 1.0 CA D:HIS229 4.8 37.8 1.0 CA D:LEU209 4.8 49.6 1.0 CB D:HIS228 4.9 37.6 1.0 O D:CYS210 4.9 49.2 1.0

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