Zinc in PDB 5sld: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1246465616

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1246465616, PDB code: 5sld 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)	69.19 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.728, 68.717, 138.389, 90, 90, 90
R / Rfree (%)	24.5 / 25.8

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1246465616 (pdb code 5sld). 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 Z1246465616, PDB code: 5sld:
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 Z1246465616


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 Z1246465616 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:27.5 occ:1.00 ND1 D:HIS264 2.0 31.7 1.0 NE2 D:HIS257 2.2 29.9 1.0 SG D:CYS279 2.2 26.5 1.0 SG D:CYS261 2.4 29.2 1.0 CE1 D:HIS264 2.9 31.6 1.0 CD2 D:HIS257 3.1 28.7 1.0 CB D:CYS261 3.1 30.7 1.0 CB D:CYS279 3.1 25.9 1.0 CG D:HIS264 3.2 31.1 1.0 CE1 D:HIS257 3.2 29.2 1.0 CB D:HIS264 3.6 34.2 1.0 NE2 D:HIS264 4.1 31.1 1.0 CG D:HIS257 4.2 27.9 1.0 CD2 D:HIS264 4.2 30.5 1.0 ND1 D:HIS257 4.3 28.6 1.0 N D:HIS264 4.4 36.1 1.0 N D:ASP415 4.6 25.6 1.0 CA D:CYS261 4.6 32.4 1.0 CA D:CYS279 4.6 24.6 1.0 CA D:HIS264 4.6 36.7 1.0 O D:HOH827 4.8 29.0 1.0 CA D:CYS414 4.9 25.4 0.4 C D:CYS261 5.0 33.1 1.0 CA D:CYS414 5.0 25.2 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 Z1246465616


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 Z1246465616 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:28.9 occ:1.00 ND1 D:HIS487 2.1 31.1 1.0 SG D:CYS484 2.3 30.6 1.0 SG D:CYS452 2.4 35.7 1.0 SG D:CYS477 2.4 26.8 1.0 CE1 D:HIS487 3.0 31.6 1.0 CG D:HIS487 3.1 29.8 1.0 CB D:CYS452 3.2 35.3 1.0 CB D:CYS477 3.2 27.4 1.0 CB D:CYS484 3.3 30.9 1.0 CB D:HIS487 3.4 28.4 1.0 CA D:CYS452 3.7 36.7 1.0 N D:CYS484 4.0 30.0 1.0 NE2 D:HIS487 4.2 31.0 1.0 CA D:CYS484 4.2 30.4 1.0 CD2 D:HIS487 4.2 30.5 1.0 N D:CYS477 4.4 27.8 1.0 CA D:CYS477 4.4 27.1 1.0 N D:HIS487 4.4 27.2 1.0 CA D:HIS487 4.6 27.3 1.0 N D:CYS452 4.6 35.4 1.0 OG1 D:THR475 4.7 26.6 1.0 CB D:THR475 4.7 26.5 1.0 C D:CYS484 4.9 30.7 1.0 O D:HOH772 4.9 27.6 1.0 O D:CYS484 5.0 30.0 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 Z1246465616


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 Z1246465616 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:35.5 occ:1.00 ND1 D:HIS229 2.0 37.3 1.0 SG D:CYS207 2.4 35.7 1.0 SG D:CYS210 2.4 39.2 1.0 SG D:CYS226 2.5 32.5 1.0 CE1 D:HIS229 2.9 37.9 1.0 CB D:CYS207 3.1 34.9 1.0 CG D:HIS229 3.2 35.3 1.0 CB D:CYS210 3.4 39.7 1.0 CB D:CYS226 3.5 30.5 1.0 CB D:HIS229 3.7 32.1 1.0 N D:CYS210 3.8 40.3 1.0 N D:CYS226 4.0 29.4 1.0 CA D:CYS210 4.1 39.6 1.0 NE2 D:HIS229 4.1 38.1 1.0 CD2 D:HIS229 4.3 37.1 1.0 C D:LEU209 4.3 40.9 1.0 CA D:CYS226 4.3 28.9 1.0 NH1 D:ARG212 4.3 36.8 1.0 N D:HIS229 4.5 30.6 1.0 CA D:CYS207 4.5 36.4 1.0 C D:CYS210 4.6 40.0 1.0 CB D:LEU209 4.7 40.5 1.0 N D:LEU209 4.7 40.3 1.0 CA D:HIS229 4.7 31.0 1.0 CA D:LEU209 4.8 40.4 1.0 CD D:ARG212 4.8 35.6 1.0 CB D:ARG212 4.9 34.2 1.0 CB D:HIS228 4.9 30.6 1.0 O D:CYS210 4.9 41.0 1.0 O D:LEU209 4.9 41.8 1.0 C D:CYS226 5.0 28.0 1.0

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