Zinc in PDB 5skw: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1272494722

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1272494722, PDB code: 5skw 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)	69.22 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.912, 67.484, 138.446, 90, 90, 90
R / Rfree (%)	19.7 / 26.7

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1272494722 (pdb code 5skw). 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 Z1272494722, PDB code: 5skw:
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 Z1272494722


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 Z1272494722 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn604 b:20.5 occ:1.00 ND1 D:HIS264 1.9 36.2 1.0 SG D:CYS279 2.2 22.1 1.0 SG D:CYS261 2.4 31.4 1.0 NE2 D:HIS257 2.4 35.5 1.0 CE1 D:HIS264 2.7 36.8 1.0 CB D:CYS261 3.0 32.2 1.0 CD2 D:HIS257 3.1 34.8 1.0 CG D:HIS264 3.1 35.2 1.0 CB D:CYS279 3.1 23.9 1.0 CE1 D:HIS257 3.5 35.6 1.0 CB D:HIS264 3.7 35.6 1.0 NE2 D:HIS264 3.9 36.6 1.0 CD2 D:HIS264 4.1 35.8 1.0 CG D:HIS257 4.3 34.1 1.0 N D:HIS264 4.4 36.0 1.0 N D:ASP415 4.4 26.2 1.0 CA D:CYS261 4.5 33.1 1.0 ND1 D:HIS257 4.5 35.7 1.0 O D:HOH720 4.6 19.7 1.0 CA D:CYS279 4.6 24.9 1.0 CA D:CYS414 4.6 25.0 0.4 CA D:HIS264 4.7 36.8 1.0 SG D:CYS414 4.7 29.2 0.6 CA D:CYS414 4.7 25.1 0.6 O D:GLY413 4.9 22.4 1.0 CB D:CYS414 4.9 25.6 0.4 C D:CYS261 5.0 33.0 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 Z1272494722


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 Z1272494722 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn605 b:24.4 occ:1.00 SG D:CYS484 2.3 37.6 1.0 ND1 D:HIS487 2.4 34.5 1.0 SG D:CYS452 2.5 46.7 1.0 SG D:CYS477 2.5 34.2 1.0 CB D:CYS452 3.2 46.0 1.0 CB D:CYS477 3.2 30.6 1.0 CE1 D:HIS487 3.3 34.8 1.0 CG D:HIS487 3.3 33.2 1.0 CB D:CYS484 3.4 36.1 1.0 CB D:HIS487 3.6 32.0 1.0 CA D:CYS452 3.8 46.1 1.0 N D:CYS484 4.0 36.4 1.0 CA D:CYS484 4.3 36.1 1.0 CA D:CYS477 4.4 30.1 1.0 N D:CYS477 4.4 31.3 1.0 NE2 D:HIS487 4.4 35.4 1.0 CD2 D:HIS487 4.5 34.4 1.0 N D:CYS452 4.6 44.4 1.0 OG1 D:THR475 4.6 31.4 1.0 N D:HIS487 4.7 32.6 1.0 CB D:THR475 4.8 30.5 1.0 CA D:HIS487 4.8 31.8 1.0 C D:CYS484 5.0 36.5 1.0 C D:CYS452 5.0 48.2 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 Z1272494722


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 Z1272494722 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn606 b:32.4 occ:1.00 ND1 D:HIS229 1.9 40.7 1.0 SG D:CYS226 2.4 44.8 1.0 SG D:CYS210 2.4 46.6 1.0 SG D:CYS207 2.4 43.7 1.0 CE1 D:HIS229 2.7 41.8 1.0 CB D:CYS207 3.1 43.0 1.0 CG D:HIS229 3.1 38.7 1.0 CB D:CYS210 3.3 45.7 1.0 CB D:CYS226 3.6 38.0 1.0 CB D:HIS229 3.7 35.4 1.0 NH1 D:ARG212 3.9 56.0 1.0 NE2 D:HIS229 3.9 41.7 1.0 N D:CYS210 4.0 45.7 1.0 N D:CYS226 4.0 36.5 1.0 CD2 D:HIS229 4.1 40.4 1.0 CA D:CYS210 4.1 45.9 1.0 CA D:CYS226 4.3 36.3 1.0 N D:HIS229 4.4 34.9 1.0 C D:LEU209 4.4 45.9 1.0 CA D:CYS207 4.6 43.4 1.0 CA D:HIS229 4.7 34.9 1.0 CB D:LEU209 4.7 46.3 1.0 C D:CYS210 4.7 46.7 1.0 CB D:ARG212 4.8 43.5 1.0 CB D:HIS228 4.8 35.0 1.0 CA D:LEU209 4.9 45.9 1.0 C D:CYS226 4.9 35.5 1.0 N D:LEU209 4.9 45.6 1.0 O D:LEU209 4.9 46.1 1.0

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