Zinc in PDB 5sm3: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z943693514

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z943693514, PDB code: 5sm3 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)	69.30 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.708, 68.101, 138.6, 90, 90, 90
R / Rfree (%)	25.7 / 30.6

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z943693514 (pdb code 5sm3). 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 Z943693514, PDB code: 5sm3:
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 Z943693514


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 Z943693514 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:52.9 occ:1.00 ND1 D:HIS264 2.2 62.8 1.0 NE2 D:HIS257 2.2 58.4 1.0 SG D:CYS279 2.3 43.8 1.0 SG D:CYS261 2.4 63.9 1.0 CB D:CYS261 3.0 59.4 1.0 CD2 D:HIS257 3.1 57.7 1.0 CG D:HIS264 3.1 61.8 1.0 CE1 D:HIS264 3.2 62.8 1.0 CB D:CYS279 3.2 44.4 1.0 CE1 D:HIS257 3.3 58.5 1.0 CB D:HIS264 3.4 62.8 1.0 CG D:HIS257 4.2 56.6 1.0 N D:HIS264 4.2 63.8 1.0 CD2 D:HIS264 4.3 62.0 1.0 ND1 D:HIS257 4.3 58.2 1.0 NE2 D:HIS264 4.3 62.7 1.0 CA D:HIS264 4.4 64.1 1.0 CA D:CYS261 4.5 59.0 1.0 O D:HOH734 4.5 63.7 1.0 CA D:CYS279 4.7 45.0 1.0 N D:ASP415 4.7 46.0 1.0 SG D:CYS414 4.9 49.1 0.6 C D:CYS261 4.9 59.5 1.0 CA D:CYS414 5.0 44.5 0.4 CA D:CYS414 5.0 45.3 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 Z943693514


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 Z943693514 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:55.6 occ:1.00 ND1 D:HIS487 2.3 52.9 1.0 SG D:CYS484 2.3 48.9 1.0 SG D:CYS452 2.5 65.9 1.0 SG D:CYS477 2.5 55.5 1.0 CE1 D:HIS487 3.2 52.6 1.0 CB D:CYS477 3.2 51.9 1.0 CB D:CYS452 3.2 67.2 1.0 CG D:HIS487 3.3 51.2 1.0 CB D:CYS484 3.3 51.6 1.0 CB D:HIS487 3.6 50.5 1.0 CA D:CYS452 3.9 68.2 1.0 N D:CYS484 4.0 53.3 1.0 CA D:CYS484 4.3 52.8 1.0 NE2 D:HIS487 4.3 52.7 1.0 CD2 D:HIS487 4.4 52.0 1.0 N D:CYS477 4.4 51.7 1.0 CA D:CYS477 4.4 51.7 1.0 N D:HIS487 4.5 50.9 1.0 N D:CYS452 4.7 66.9 1.0 CA D:HIS487 4.7 50.8 1.0 CB D:THR475 4.8 51.2 1.0 OG1 D:THR475 4.8 52.6 1.0 O D:CYS484 4.9 53.6 1.0 O D:HOH789 4.9 44.5 1.0 C D:CYS484 4.9 53.7 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 Z943693514


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 Z943693514 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:60.5 occ:1.00 ND1 D:HIS229 1.9 60.9 1.0 SG D:CYS210 2.4 69.1 1.0 SG D:CYS207 2.4 68.8 1.0 SG D:CYS226 2.5 62.0 1.0 CE1 D:HIS229 2.7 61.6 1.0 CB D:CYS207 3.1 67.5 1.0 CG D:HIS229 3.2 59.3 1.0 CB D:CYS210 3.2 68.0 1.0 CB D:CYS226 3.5 56.3 1.0 N D:CYS210 3.7 68.3 1.0 CB D:HIS229 3.7 57.5 1.0 NE2 D:HIS229 3.9 61.6 1.0 CA D:CYS210 4.0 67.9 1.0 N D:CYS226 4.0 55.4 1.0 CD2 D:HIS229 4.1 60.5 1.0 C D:LEU209 4.3 69.2 1.0 CA D:CYS226 4.4 55.1 1.0 N D:HIS229 4.5 56.7 1.0 NH1 D:ARG212 4.5 65.8 1.0 C D:CYS210 4.6 67.8 1.0 CA D:CYS207 4.6 67.6 1.0 CB D:LEU209 4.7 70.5 1.0 CD D:ARG212 4.8 63.4 1.0 CA D:HIS229 4.8 56.9 1.0 N D:LEU209 4.8 69.8 1.0 CA D:LEU209 4.8 69.8 1.0 CB D:ARG212 4.9 62.2 1.0 O D:CYS210 4.9 68.2 1.0 CB D:HIS228 4.9 56.4 1.0 O D:LEU209 4.9 69.3 1.0

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