Zinc in PDB 5slu: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1796014543

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1796014543, PDB code: 5slu 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)	69.25 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.929, 68.436, 138.492, 90, 90, 90
R / Rfree (%)	24.3 / 28.3

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1796014543 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1796014543 (pdb code 5slu). 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 Z1796014543, PDB code: 5slu:
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 Z1796014543


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 Z1796014543 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:44.0 occ:1.00 ND1 D:HIS264 2.0 57.4 1.0 NE2 D:HIS257 2.2 48.5 1.0 SG D:CYS279 2.3 40.4 1.0 SG D:CYS261 2.3 54.0 1.0 CE1 D:HIS264 2.9 58.1 1.0 CB D:CYS261 3.0 52.1 1.0 CD2 D:HIS257 3.1 48.1 1.0 CG D:HIS264 3.1 55.8 1.0 CB D:CYS279 3.1 40.9 1.0 CE1 D:HIS257 3.3 48.6 1.0 CB D:HIS264 3.5 55.4 1.0 NE2 D:HIS264 4.1 57.8 1.0 CD2 D:HIS264 4.2 56.7 1.0 CG D:HIS257 4.2 47.8 1.0 N D:HIS264 4.3 55.3 1.0 ND1 D:HIS257 4.3 48.6 1.0 CA D:CYS261 4.5 52.2 1.0 CA D:HIS264 4.5 55.9 1.0 CA D:CYS279 4.6 41.8 1.0 N D:ASP415 4.7 40.8 1.0 O D:HOH749 4.8 50.9 1.0 C D:CYS261 4.9 53.0 1.0 O D:CYS261 4.9 52.9 1.0 CA D:CYS414 5.0 40.9 0.4 CA D:MET276 5.0 40.1 1.0 SG D:CYS414 5.0 45.8 0.6 CA D:CYS414 5.0 41.2 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 Z1796014543


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 Z1796014543 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:50.0 occ:1.00 ND1 D:HIS487 2.2 48.7 1.0 SG D:CYS484 2.2 47.6 1.0 SG D:CYS452 2.3 57.3 1.0 SG D:CYS477 2.4 51.9 1.0 CE1 D:HIS487 3.0 48.6 1.0 CB D:CYS452 3.2 62.0 1.0 CB D:CYS477 3.2 48.9 1.0 CG D:HIS487 3.3 46.9 1.0 CB D:CYS484 3.3 49.4 1.0 CB D:HIS487 3.7 46.2 1.0 CA D:CYS452 3.8 63.8 1.0 N D:CYS484 4.0 49.6 1.0 NE2 D:HIS487 4.2 48.3 1.0 CA D:CYS484 4.2 49.5 1.0 CD2 D:HIS487 4.3 47.6 1.0 N D:CYS477 4.4 47.5 1.0 CA D:CYS477 4.4 48.2 1.0 N D:HIS487 4.5 47.0 1.0 N D:CYS452 4.5 62.6 1.0 CA D:HIS487 4.7 46.6 1.0 CB D:THR475 4.8 43.2 1.0 O D:CYS484 4.8 50.6 1.0 OG1 D:THR475 4.8 43.7 1.0 C D:CYS484 4.9 49.9 1.0 O D:HOH802 4.9 43.1 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 Z1796014543


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 Z1796014543 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:57.3 occ:1.00 ND1 D:HIS229 1.9 53.3 1.0 SG D:CYS207 2.4 61.2 1.0 SG D:CYS210 2.4 59.9 1.0 SG D:CYS226 2.5 55.1 1.0 CE1 D:HIS229 2.7 53.4 1.0 CB D:CYS207 3.0 61.2 1.0 CG D:HIS229 3.2 51.6 1.0 CB D:CYS210 3.4 59.1 1.0 CB D:CYS226 3.5 48.4 1.0 CB D:HIS229 3.7 49.4 1.0 N D:CYS210 3.8 59.7 1.0 NE2 D:HIS229 4.0 53.6 1.0 N D:CYS226 4.0 47.3 1.0 CA D:CYS210 4.1 59.2 1.0 CD2 D:HIS229 4.2 52.4 1.0 CA D:CYS226 4.3 46.6 1.0 NH1 D:ARG212 4.4 59.9 1.0 C D:LEU209 4.4 60.9 1.0 CA D:CYS207 4.5 61.5 1.0 N D:HIS229 4.5 47.7 1.0 CB D:ARG212 4.6 55.3 1.0 C D:CYS210 4.7 59.1 1.0 CB D:LEU209 4.7 62.0 1.0 CD D:ARG212 4.7 56.9 1.0 CA D:HIS229 4.8 48.5 1.0 CA D:LEU209 4.9 61.6 1.0 N D:LEU209 4.9 62.1 1.0 CG D:ARG212 4.9 56.0 1.0

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