Zinc in PDB 5slr: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2073741691

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2073741691, PDB code: 5slr 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)	25.68 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.827, 67.703, 138.736, 90, 90, 90
R / Rfree (%)	23.6 / 26.7

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2073741691 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 Z2073741691 (pdb code 5slr). 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 Z2073741691, PDB code: 5slr:
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 Z2073741691


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 Z2073741691 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:35.8 occ:1.00 ND1 D:HIS264 1.9 43.3 1.0 NE2 D:HIS257 2.2 39.2 1.0 SG D:CYS279 2.3 34.8 1.0 SG D:CYS261 2.3 42.2 1.0 CE1 D:HIS264 2.9 43.7 1.0 CG D:HIS264 3.0 42.9 1.0 CD2 D:HIS257 3.1 38.0 1.0 CB D:CYS261 3.1 42.9 1.0 CB D:CYS279 3.1 31.3 1.0 CE1 D:HIS257 3.2 39.5 1.0 CB D:HIS264 3.5 45.1 1.0 NE2 D:HIS264 4.0 43.5 1.0 CD2 D:HIS264 4.1 42.6 1.0 CG D:HIS257 4.2 38.5 1.0 ND1 D:HIS257 4.3 39.7 1.0 N D:HIS264 4.3 46.4 1.0 CA D:HIS264 4.5 47.2 1.0 N D:ASP415 4.5 35.7 1.0 CA D:CYS261 4.6 44.2 1.0 CA D:CYS279 4.6 31.5 1.0 CA D:CYS414 4.9 35.2 0.4 CA D:CYS414 5.0 35.2 0.6 SG D:CYS414 5.0 36.6 0.6 C D:CYS261 5.0 44.8 1.0 O D:HOH823 5.0 35.1 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 Z2073741691


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 Z2073741691 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:42.4 occ:1.00 ND1 D:HIS487 2.2 39.7 1.0 SG D:CYS484 2.3 41.1 1.0 SG D:CYS452 2.4 53.1 1.0 SG D:CYS477 2.4 41.3 1.0 CB D:CYS477 3.1 39.8 1.0 CB D:CYS452 3.2 57.3 1.0 CE1 D:HIS487 3.2 39.8 1.0 CG D:HIS487 3.2 38.3 1.0 CB D:CYS484 3.3 41.3 1.0 CB D:HIS487 3.5 37.0 1.0 CA D:CYS452 3.8 58.7 1.0 N D:CYS484 4.0 41.4 1.0 CA D:CYS484 4.2 41.2 1.0 N D:CYS477 4.3 39.5 1.0 CA D:CYS477 4.3 39.7 1.0 NE2 D:HIS487 4.3 39.8 1.0 CD2 D:HIS487 4.4 39.2 1.0 N D:HIS487 4.5 36.9 1.0 N D:CYS452 4.6 56.5 1.0 CA D:HIS487 4.6 37.0 1.0 OG1 D:THR475 4.7 37.8 1.0 CB D:THR475 4.7 36.5 1.0 O D:CYS484 4.9 42.0 1.0 C D:CYS484 4.9 41.8 1.0 C D:CYS452 5.0 62.7 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 Z2073741691


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 Z2073741691 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:50.4 occ:1.00 ND1 D:HIS229 2.0 47.0 1.0 SG D:CYS207 2.3 55.1 1.0 SG D:CYS210 2.4 52.2 1.0 SG D:CYS226 2.4 47.5 1.0 CE1 D:HIS229 2.8 47.4 1.0 CB D:CYS207 3.1 54.1 1.0 CG D:HIS229 3.1 45.2 1.0 CB D:CYS210 3.5 52.3 1.0 CB D:CYS226 3.5 41.7 1.0 CB D:HIS229 3.6 42.6 1.0 N D:CYS210 3.8 53.4 1.0 N D:CYS226 4.0 41.2 1.0 NE2 D:HIS229 4.0 47.6 1.0 CA D:CYS210 4.1 52.5 1.0 CD2 D:HIS229 4.2 46.4 1.0 NH1 D:ARG212 4.3 53.0 1.0 CA D:CYS226 4.3 40.7 1.0 C D:LEU209 4.4 54.6 1.0 N D:HIS229 4.4 41.9 1.0 CA D:CYS207 4.5 54.3 1.0 CB D:LEU209 4.6 55.5 1.0 C D:CYS210 4.6 52.1 1.0 CA D:HIS229 4.7 42.0 1.0 CB D:ARG212 4.7 47.2 1.0 N D:LEU209 4.8 55.2 1.0 O D:CYS210 4.8 52.8 1.0 CA D:LEU209 4.8 55.1 1.0 CD D:ARG212 4.9 49.9 1.0 CB D:HIS228 4.9 41.9 1.0

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