Zinc in PDB 5sli: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540, PDB code: 5sli 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)	69.67 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.758, 69.462, 139.336, 90, 90, 90
R / Rfree (%)	20.8 / 27.1

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540 (pdb code 5sli). 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 Z1003146540, PDB code: 5sli:
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 Z1003146540


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 Z1003146540 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:41.9 occ:1.00 ND1 D:HIS264 2.0 40.9 1.0 NE2 D:HIS257 2.1 54.2 1.0 SG D:CYS279 2.3 38.3 1.0 SG D:CYS261 2.3 50.9 1.0 CE1 D:HIS264 2.5 43.2 1.0 CD2 D:HIS257 3.0 48.8 1.0 CB D:CYS261 3.1 50.0 1.0 CE1 D:HIS257 3.2 49.3 1.0 CB D:CYS279 3.2 36.2 1.0 CG D:HIS264 3.2 43.5 1.0 NE2 D:HIS264 3.8 44.2 1.0 CB D:HIS264 3.9 49.5 1.0 CD2 D:HIS264 4.1 43.9 1.0 CG D:HIS257 4.2 49.6 1.0 ND1 D:HIS257 4.2 51.6 1.0 O D:HOH865 4.4 52.6 1.0 N D:ASP415 4.5 43.0 1.0 N D:HIS264 4.5 47.4 1.0 CA D:CYS261 4.6 49.5 1.0 CA D:CYS279 4.6 34.6 1.0 CA D:HIS264 4.8 47.8 1.0 CA D:CYS414 5.0 46.4 0.4

Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540


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 Z1003146540 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:42.3 occ:1.00 SG D:CYS452 2.2 53.5 1.0 SG D:CYS484 2.2 41.0 1.0 SG D:CYS477 2.2 48.3 1.0 ND1 D:HIS487 2.3 43.0 1.0 CB D:CYS452 2.9 56.1 1.0 CB D:CYS477 3.1 45.6 1.0 CE1 D:HIS487 3.1 43.1 1.0 CB D:CYS484 3.2 42.6 1.0 CG D:HIS487 3.3 40.5 1.0 CA D:CYS452 3.6 57.6 1.0 CB D:HIS487 3.6 41.4 1.0 N D:CYS484 3.9 44.0 1.0 CA D:CYS484 4.1 43.3 1.0 NE2 D:HIS487 4.2 40.0 1.0 N D:CYS452 4.3 56.9 1.0 CD2 D:HIS487 4.3 39.7 1.0 CA D:CYS477 4.3 45.9 1.0 N D:CYS477 4.3 47.0 1.0 CB D:THR475 4.6 38.0 1.0 N D:HIS487 4.7 47.4 1.0 CA D:HIS487 4.8 43.3 1.0 C D:CYS484 4.8 46.7 1.0 OG1 D:THR475 4.8 32.5 1.0 C D:CYS452 4.9 59.4 1.0 O D:CYS484 5.0 45.2 1.0 CG2 D:THR475 5.0 37.1 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 Z1003146540


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 Z1003146540 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:46.3 occ:1.00 ND1 D:HIS229 1.8 42.6 1.0 SG D:CYS207 2.3 43.2 1.0 SG D:CYS226 2.3 45.5 1.0 SG D:CYS210 2.4 43.6 1.0 CE1 D:HIS229 2.7 47.2 1.0 CB D:CYS207 2.9 43.3 1.0 CG D:HIS229 2.9 40.5 1.0 CB D:CYS226 3.3 40.9 1.0 CB D:CYS210 3.4 45.4 1.0 CB D:HIS229 3.4 38.5 1.0 N D:CYS210 3.8 46.7 1.0 NE2 D:HIS229 3.9 42.8 1.0 N D:CYS226 3.9 43.6 1.0 CD2 D:HIS229 4.0 40.1 1.0 CA D:CYS210 4.1 45.4 1.0 NH1 D:ARG212 4.2 68.2 1.0 CA D:CYS226 4.2 41.0 1.0 C D:LEU209 4.2 48.8 1.0 CA D:CYS207 4.4 45.3 1.0 N D:HIS229 4.5 43.4 1.0 CB D:LEU209 4.5 50.8 1.0 CA D:HIS229 4.6 41.4 1.0 C D:CYS210 4.7 46.9 1.0 CB D:ARG212 4.7 54.9 1.0 CA D:LEU209 4.8 50.0 1.0 O D:LEU209 4.8 55.4 1.0 N D:LEU209 4.8 51.8 1.0 CD D:ARG212 4.8 60.8 1.0 C D:CYS226 4.9 41.3 1.0 CG D:ARG212 5.0 59.3 1.0 O D:CYS210 5.0 43.6 1.0

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