Zinc in PDB 5sm4: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434944

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434944, PDB code: 5sm4 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)	69.26 / 2.16
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.54, 67.42, 138.52, 90, 90, 90
R / Rfree (%)	22.9 / 27.1

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434944 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 Z2856434944 (pdb code 5sm4). 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 Z2856434944, PDB code: 5sm4:
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 Z2856434944


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 Z2856434944 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:42.6 occ:1.00 ND1 D:HIS264 1.9 49.7 1.0 NE2 D:HIS257 2.2 47.0 1.0 SG D:CYS279 2.3 39.7 1.0 SG D:CYS261 2.4 50.3 1.0 CE1 D:HIS264 2.9 49.8 1.0 CG D:HIS264 3.0 49.3 1.0 CB D:CYS279 3.1 39.6 1.0 CD2 D:HIS257 3.1 46.5 1.0 CB D:CYS261 3.2 50.1 1.0 CE1 D:HIS257 3.3 47.2 1.0 CB D:HIS264 3.4 50.0 1.0 NE2 D:HIS264 4.0 49.8 1.0 CD2 D:HIS264 4.1 49.2 1.0 CG D:HIS257 4.3 46.0 1.0 ND1 D:HIS257 4.4 47.4 1.0 N D:HIS264 4.4 51.7 1.0 CA D:HIS264 4.5 52.0 1.0 CA D:CYS279 4.6 40.1 1.0 N D:ASP415 4.6 40.4 1.0 CA D:CYS261 4.6 50.6 1.0 O D:HOH749 4.9 42.5 1.0 CA D:CYS414 4.9 40.3 0.6 SG D:CYS414 4.9 45.3 0.6 CA D:CYS414 5.0 40.1 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 Z2856434944


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 Z2856434944 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:46.4 occ:1.00 ND1 D:HIS487 2.1 41.6 1.0 SG D:CYS484 2.3 41.6 1.0 SG D:CYS477 2.4 46.7 1.0 SG D:CYS452 2.5 50.5 1.0 CE1 D:HIS487 3.0 42.0 1.0 CG D:HIS487 3.2 40.7 1.0 CB D:CYS477 3.3 43.2 1.0 CB D:CYS452 3.3 53.6 1.0 CB D:CYS484 3.3 42.3 1.0 CB D:HIS487 3.6 39.8 1.0 CA D:CYS452 3.8 55.3 1.0 N D:CYS484 4.1 44.0 1.0 NE2 D:HIS487 4.2 42.9 1.0 CA D:CYS484 4.3 43.1 1.0 CD2 D:HIS487 4.3 42.1 1.0 N D:CYS477 4.4 43.6 1.0 CA D:CYS477 4.4 43.1 1.0 N D:HIS487 4.5 40.5 1.0 N D:CYS452 4.6 54.1 1.0 CA D:HIS487 4.7 40.3 1.0 CB D:THR475 4.7 40.6 1.0 OG1 D:THR475 4.7 41.3 1.0 O D:HOH798 4.9 34.0 1.0 C D:CYS484 4.9 44.0 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 Z2856434944


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 Z2856434944 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:50.9 occ:1.00 ND1 D:HIS229 1.9 52.1 1.0 SG D:CYS207 2.3 58.8 1.0 SG D:CYS210 2.4 57.5 1.0 SG D:CYS226 2.5 49.1 1.0 CE1 D:HIS229 2.7 52.5 1.0 CB D:CYS207 3.0 56.6 1.0 CG D:HIS229 3.1 50.2 1.0 CB D:CYS210 3.5 56.4 1.0 CB D:CYS226 3.6 44.7 1.0 CB D:HIS229 3.7 47.3 1.0 N D:CYS210 3.8 55.8 1.0 NE2 D:HIS229 3.9 52.5 1.0 N D:CYS226 4.0 44.2 1.0 CA D:CYS210 4.1 56.0 1.0 CD2 D:HIS229 4.1 51.5 1.0 NH1 D:ARG212 4.3 59.7 1.0 C D:LEU209 4.3 56.4 1.0 CA D:CYS226 4.4 43.9 1.0 N D:HIS229 4.4 45.7 1.0 CA D:CYS207 4.5 56.5 1.0 CB D:LEU209 4.6 56.2 1.0 CA D:HIS229 4.7 46.4 1.0 N D:LEU209 4.7 56.7 1.0 CA D:LEU209 4.8 56.3 1.0 C D:CYS210 4.8 56.5 1.0 CB D:ARG212 4.8 53.6 1.0 CB D:HIS228 4.9 45.4 1.0 CD D:ARG212 5.0 55.7 1.0 C D:CYS226 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.