Zinc in PDB 5sl7: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1186029914

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1186029914, PDB code: 5sl7 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 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.686, 68.31, 138.449, 90, 90, 90
R / Rfree (%)	22.6 / 25.1

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1186029914 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1186029914 (pdb code 5sl7). 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 Z1186029914, PDB code: 5sl7:
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 Z1186029914


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 Z1186029914 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:32.1 occ:1.00 ND1 D:HIS264 2.0 36.4 1.0 NE2 D:HIS257 2.2 37.0 1.0 SG D:CYS279 2.3 31.3 1.0 SG D:CYS261 2.4 35.3 1.0 CE1 D:HIS264 2.8 36.7 1.0 CD2 D:HIS257 3.0 36.1 1.0 CG D:HIS264 3.1 36.4 1.0 CB D:CYS279 3.1 27.7 1.0 CB D:CYS261 3.1 36.5 1.0 CE1 D:HIS257 3.3 36.9 1.0 CB D:HIS264 3.5 40.3 1.0 NE2 D:HIS264 4.0 37.0 1.0 CD2 D:HIS264 4.2 36.3 1.0 CG D:HIS257 4.2 35.6 1.0 ND1 D:HIS257 4.3 36.8 1.0 N D:HIS264 4.4 42.5 1.0 CA D:CYS261 4.6 38.4 1.0 CA D:HIS264 4.6 43.0 1.0 CA D:CYS279 4.6 28.0 1.0 N D:ASP415 4.6 31.7 1.0 SG D:CYS414 4.9 36.2 0.6 O D:HOH785 5.0 30.8 1.0 CA D:CYS414 5.0 31.7 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 Z1186029914


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 Z1186029914 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:36.4 occ:1.00 ND1 D:HIS487 2.2 33.4 1.0 SG D:CYS484 2.3 34.9 1.0 SG D:CYS452 2.3 43.3 1.0 SG D:CYS477 2.4 34.9 1.0 CE1 D:HIS487 3.2 33.3 1.0 CG D:HIS487 3.2 32.3 1.0 CB D:CYS452 3.2 47.1 1.0 CB D:CYS477 3.2 33.1 1.0 CB D:CYS484 3.3 35.0 1.0 CB D:HIS487 3.5 31.5 1.0 CA D:CYS452 3.8 48.7 1.0 N D:CYS484 4.0 34.9 1.0 CA D:CYS484 4.3 35.0 1.0 NE2 D:HIS487 4.3 33.5 1.0 N D:CYS477 4.3 33.3 1.0 CD2 D:HIS487 4.3 32.9 1.0 CA D:CYS477 4.4 32.9 1.0 N D:HIS487 4.5 32.1 1.0 N D:CYS452 4.5 46.9 1.0 CA D:HIS487 4.6 31.5 1.0 OG1 D:THR475 4.7 31.4 1.0 CB D:THR475 4.7 30.5 1.0 O D:CYS484 4.9 35.7 1.0 C D:CYS484 4.9 35.8 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 Z1186029914


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 Z1186029914 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:43.4 occ:1.00 ND1 D:HIS229 1.9 42.7 1.0 SG D:CYS207 2.3 47.9 1.0 SG D:CYS210 2.3 45.7 1.0 SG D:CYS226 2.4 39.8 1.0 CE1 D:HIS229 2.8 43.2 1.0 CB D:CYS207 3.0 45.7 1.0 CG D:HIS229 3.1 40.5 1.0 CB D:CYS210 3.4 45.9 1.0 CB D:CYS226 3.5 36.3 1.0 CB D:HIS229 3.7 37.1 1.0 N D:CYS210 3.8 46.6 1.0 N D:CYS226 3.9 35.7 1.0 NE2 D:HIS229 4.0 43.4 1.0 CA D:CYS210 4.1 46.1 1.0 CD2 D:HIS229 4.2 42.1 1.0 NH1 D:ARG212 4.2 46.3 1.0 CA D:CYS226 4.3 35.2 1.0 C D:LEU209 4.4 47.6 1.0 N D:HIS229 4.5 36.2 1.0 CA D:CYS207 4.5 45.9 1.0 C D:CYS210 4.7 46.9 1.0 CB D:LEU209 4.7 48.2 1.0 CD D:ARG212 4.7 43.1 1.0 CA D:HIS229 4.7 36.4 1.0 CB D:ARG212 4.8 42.1 1.0 N D:LEU209 4.8 47.5 1.0 CA D:LEU209 4.8 47.8 1.0 CB D:HIS228 4.9 36.6 1.0 O D:CYS210 4.9 47.3 1.0 C D:CYS226 5.0 33.8 1.0

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