Zinc in PDB 5smk: Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 NSP14

The structure of Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 NSP14, PDB code: 5smk 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)	69.31 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.538, 68.093, 138.425, 90, 90, 90
R / Rfree (%)	19.1 / 21.7

The binding sites of Zinc atom in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 NSP14 (pdb code 5smk). 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 of Ground-State Model of Sars-Cov-2 NSP14, PDB code: 5smk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 NSP14


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 of Ground-State Model of Sars-Cov-2 NSP14 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:16.0 occ:1.00 ND1 D:HIS264 1.9 18.6 1.0 NE2 D:HIS257 2.1 17.4 1.0 SG D:CYS279 2.3 15.4 1.0 SG D:CYS261 2.4 18.2 1.0 CE1 D:HIS264 2.8 18.5 1.0 CG D:HIS264 3.0 20.7 1.0 CD2 D:HIS257 3.1 18.8 1.0 CB D:CYS279 3.1 13.7 1.0 CE1 D:HIS257 3.1 17.7 1.0 CB D:CYS261 3.2 20.2 1.0 CB D:HIS264 3.5 23.7 1.0 NE2 D:HIS264 4.0 19.9 1.0 CD2 D:HIS264 4.1 19.7 1.0 ND1 D:HIS257 4.2 17.3 1.0 CG D:HIS257 4.2 18.4 1.0 N D:HIS264 4.3 26.2 1.0 N D:ASP415 4.5 17.7 1.0 CA D:HIS264 4.5 26.9 1.0 CA D:CYS279 4.5 13.6 1.0 CA D:CYS261 4.6 20.6 1.0 CA D:CYS414 4.9 17.1 0.6 CA D:CYS414 4.9 16.5 0.4 SG D:CYS414 5.0 18.7 0.6 C D:CYS261 5.0 21.6 1.0 O D:HOH761 5.0 22.3 1.0

Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 NSP14


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 of Ground-State Model of Sars-Cov-2 NSP14 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:17.9 occ:1.00 ND1 D:HIS487 2.1 17.5 1.0 SG D:CYS484 2.3 18.6 1.0 SG D:CYS477 2.3 15.9 1.0 SG D:CYS452 2.4 26.1 1.0 CG D:HIS487 3.1 18.1 1.0 CE1 D:HIS487 3.1 18.3 1.0 CB D:CYS452 3.2 28.1 1.0 CB D:CYS477 3.2 17.1 1.0 CB D:CYS484 3.3 19.6 1.0 CB D:HIS487 3.4 17.9 1.0 CA D:CYS452 3.8 33.3 1.0 N D:CYS484 3.9 17.6 1.0 CA D:CYS484 4.2 18.0 1.0 CD2 D:HIS487 4.2 17.5 1.0 NE2 D:HIS487 4.2 17.9 1.0 N D:CYS477 4.4 18.8 1.0 CA D:CYS477 4.4 18.6 1.0 N D:HIS487 4.5 19.0 1.0 N D:CYS452 4.5 29.9 1.0 CA D:HIS487 4.5 18.6 1.0 CB D:THR475 4.6 16.5 1.0 OG1 D:THR475 4.7 17.2 1.0 O D:CYS484 4.8 18.4 1.0 C D:CYS484 4.8 21.0 1.0

Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 NSP14


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 of Ground-State Model of Sars-Cov-2 NSP14 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:26.7 occ:1.00 ND1 D:HIS229 1.9 24.3 1.0 SG D:CYS207 2.3 26.5 1.0 SG D:CYS210 2.4 28.7 1.0 SG D:CYS226 2.5 22.9 1.0 CE1 D:HIS229 2.7 24.7 1.0 CB D:CYS207 3.0 26.9 1.0 CG D:HIS229 3.1 22.9 1.0 CB D:CYS210 3.4 28.4 1.0 CB D:CYS226 3.6 20.6 1.0 CB D:HIS229 3.6 21.8 1.0 N D:CYS210 3.8 28.6 1.0 NE2 D:HIS229 4.0 24.9 1.0 N D:CYS226 4.0 19.9 1.0 CA D:CYS210 4.1 27.8 1.0 CD2 D:HIS229 4.1 24.6 1.0 NH1 D:ARG212 4.2 27.1 1.0 C D:LEU209 4.3 29.1 1.0 CA D:CYS226 4.4 19.3 1.0 CA D:CYS207 4.5 29.0 1.0 N D:HIS229 4.5 21.3 1.0 CB D:LEU209 4.6 28.3 1.0 C D:CYS210 4.7 29.4 1.0 CA D:HIS229 4.7 21.3 1.0 N D:LEU209 4.7 30.4 1.0 CB D:HIS228 4.8 21.6 1.0 CB D:ARG212 4.8 28.1 1.0 CA D:LEU209 4.8 29.3 1.0 CD D:ARG212 4.9 25.6 1.0 O D:CYS210 4.9 33.1 1.0 O D:LEU209 5.0 30.6 1.0 C D:CYS226 5.0 17.5 1.0

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