Zinc in PDB 5sma: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434890

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434890, PDB code: 5sma 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)	69.29 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.259, 67.716, 138.575, 90, 90, 90
R / Rfree (%)	22.7 / 25.9

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434890 (pdb code 5sma). 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 Z2856434890, PDB code: 5sma:
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 Z2856434890


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 Z2856434890 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:32.0 occ:1.00 ND1 D:HIS264 2.0 41.7 1.0 NE2 D:HIS257 2.2 40.1 1.0 SG D:CYS279 2.2 30.7 1.0 SG D:CYS261 2.4 38.8 1.0 CE1 D:HIS264 2.9 42.5 1.0 CG D:HIS264 3.0 41.2 1.0 CB D:CYS279 3.1 29.4 1.0 CD2 D:HIS257 3.1 38.8 1.0 CB D:CYS261 3.1 40.5 1.0 CE1 D:HIS257 3.3 40.0 1.0 CB D:HIS264 3.4 42.5 1.0 NE2 D:HIS264 4.1 42.4 1.0 CD2 D:HIS264 4.1 41.4 1.0 CG D:HIS257 4.2 38.4 1.0 N D:HIS264 4.3 43.9 1.0 ND1 D:HIS257 4.3 40.0 1.0 CA D:HIS264 4.5 44.5 1.0 CA D:CYS279 4.5 29.1 1.0 CA D:CYS261 4.6 41.5 1.0 N D:ASP415 4.6 32.3 1.0 O D:HOH773 4.9 32.0 1.0 SG D:CYS414 5.0 32.8 0.6 C D:CYS261 5.0 42.5 1.0 CA D:CYS414 5.0 32.1 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 Z2856434890


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 Z2856434890 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:38.4 occ:1.00 ND1 D:HIS487 2.1 36.9 1.0 SG D:CYS484 2.3 35.8 1.0 SG D:CYS452 2.4 44.5 1.0 SG D:CYS477 2.4 35.4 1.0 CE1 D:HIS487 3.0 37.3 1.0 CG D:HIS487 3.2 35.4 1.0 CB D:CYS477 3.2 33.5 1.0 CB D:CYS452 3.2 47.2 1.0 CB D:CYS484 3.3 35.3 1.0 CB D:HIS487 3.6 33.3 1.0 CA D:CYS452 3.8 48.3 1.0 N D:CYS484 4.1 35.5 1.0 NE2 D:HIS487 4.2 37.4 1.0 CA D:CYS484 4.3 35.3 1.0 CD2 D:HIS487 4.3 36.2 1.0 N D:CYS477 4.3 33.5 1.0 CA D:CYS477 4.4 33.2 1.0 N D:HIS487 4.6 33.0 1.0 N D:CYS452 4.6 47.0 1.0 CA D:HIS487 4.7 32.9 1.0 CB D:THR475 4.7 32.0 1.0 OG1 D:THR475 4.8 32.1 1.0 C D:CYS484 4.9 36.0 1.0 O D:CYS484 5.0 36.1 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 Z2856434890


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 Z2856434890 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:42.5 occ:1.00 ND1 D:HIS229 2.0 40.6 1.0 SG D:CYS207 2.3 46.3 1.0 SG D:CYS210 2.4 47.0 1.0 SG D:CYS226 2.5 41.0 1.0 CE1 D:HIS229 2.8 40.8 1.0 CB D:CYS207 3.0 45.6 1.0 CG D:HIS229 3.2 38.6 1.0 CB D:CYS226 3.5 36.6 1.0 CB D:CYS210 3.5 46.2 1.0 CB D:HIS229 3.7 36.7 1.0 N D:CYS210 3.8 46.0 1.0 N D:CYS226 3.9 36.5 1.0 NE2 D:HIS229 4.0 40.8 1.0 NH1 D:ARG212 4.1 49.8 1.0 CA D:CYS210 4.1 46.0 1.0 CD2 D:HIS229 4.2 39.9 1.0 CA D:CYS226 4.3 35.8 1.0 C D:LEU209 4.4 46.6 1.0 CA D:CYS207 4.4 46.0 1.0 N D:HIS229 4.5 35.9 1.0 CB D:LEU209 4.6 46.9 1.0 C D:CYS210 4.7 46.4 1.0 CA D:HIS229 4.7 36.4 1.0 CB D:ARG212 4.8 44.2 1.0 N D:LEU209 4.8 46.5 1.0 CA D:LEU209 4.8 46.6 1.0 CD D:ARG212 4.9 45.7 1.0 CB D:HIS228 4.9 34.3 1.0 O D:CYS210 4.9 46.9 1.0 C D:CYS226 5.0 34.0 1.0

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