Zinc in PDB 7r2v: Structure of NSP14 From Sars-Cov-2 in Complex with Sah

The structure of Structure of NSP14 From Sars-Cov-2 in Complex with Sah, PDB code: 7r2v was solved by A.Czarna, J.Plewka, L.Kresik, A.Matsuda, K.Abdulkarim, C.Robinson, S.Obyrne, F.Cunningham, I.Georgiou, M.Pachota, G.M.Popowicz, P.G.Wyatt, G.Dubin, K.Pyrc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.176, 100.312, 90.874, 90, 107.66, 90
R / Rfree (%)	19.6 / 25.4

The binding sites of Zinc atom in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah (pdb code 7r2v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah, PDB code: 7r2v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:77.3 occ:1.00 SG A:CYS484 2.1 82.7 1.0 ND1 A:HIS487 2.2 87.2 1.0 SG A:CYS477 2.3 83.7 1.0 SG A:CYS452 2.7 84.8 1.0 CE1 A:HIS487 3.0 88.0 1.0 CG A:HIS487 3.2 85.0 1.0 CB A:CYS452 3.2 89.3 1.0 CB A:CYS484 3.3 80.9 1.0 CB A:CYS477 3.3 82.3 1.0 CB A:HIS487 3.6 82.7 1.0 N A:CYS484 3.8 83.2 1.0 CA A:CYS452 3.9 91.2 1.0 CA A:CYS484 4.1 80.5 1.0 NE2 A:HIS487 4.1 87.1 1.0 CD2 A:HIS487 4.2 84.6 1.0 N A:CYS477 4.4 80.9 1.0 CA A:CYS477 4.5 84.0 1.0 CB A:THR475 4.6 69.6 1.0 OG1 A:THR475 4.7 66.2 1.0 N A:HIS487 4.7 84.5 1.0 CA A:HIS487 4.8 81.5 1.0 O A:CYS484 4.8 70.7 1.0 C A:CYS484 4.9 76.4 1.0 C A:VAL483 4.9 88.0 1.0 O A:PRO451 4.9 90.1 1.0 C A:CYS452 4.9 95.1 1.0 N A:CYS452 4.9 89.3 1.0

Zinc binding site 2 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:40.6 occ:1.00 ND1 A:HIS229 1.9 45.3 1.0 SG A:CYS210 2.1 44.6 1.0 SG A:CYS226 2.2 35.3 1.0 SG A:CYS207 2.4 38.9 1.0 CE1 A:HIS229 2.8 46.8 1.0 CG A:HIS229 3.1 45.4 1.0 CB A:CYS207 3.2 41.9 1.0 CB A:CYS210 3.5 47.2 1.0 CB A:CYS226 3.5 37.0 1.0 CB A:HIS229 3.5 43.8 1.0 N A:CYS210 3.8 49.7 1.0 N A:CYS226 3.9 40.0 1.0 NE2 A:HIS229 4.0 48.6 1.0 CD2 A:HIS229 4.1 47.3 1.0 CA A:CYS210 4.2 47.4 1.0 CA A:CYS226 4.3 37.9 1.0 N A:HIS229 4.4 41.1 1.0 C A:LEU209 4.5 54.3 1.0 CB A:ARG212 4.5 42.2 1.0 NH1 A:ARG212 4.6 45.7 1.0 CA A:HIS229 4.6 42.4 1.0 CB A:LEU209 4.6 54.4 1.0 C A:CYS210 4.7 47.9 1.0 CA A:CYS207 4.7 43.5 1.0 N A:LEU209 4.8 53.3 1.0 CD A:ARG212 4.8 44.0 1.0 O A:CYS210 4.8 50.2 1.0 CA A:LEU209 4.9 53.5 1.0 C A:CYS226 4.9 37.2 1.0 CB A:HIS228 4.9 39.2 1.0 C A:ALA225 4.9 43.0 1.0 CG A:ARG212 5.0 43.1 1.0

Zinc binding site 3 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:45.5 occ:1.00 ND1 A:HIS264 1.9 46.2 1.0 NE2 A:HIS257 2.1 41.9 1.0 SG A:CYS261 2.2 46.7 1.0 SG A:CYS279 2.2 33.1 1.0 CE1 A:HIS264 2.9 45.9 1.0 CG A:HIS264 3.0 48.6 1.0 CE1 A:HIS257 3.0 43.2 1.0 CB A:CYS279 3.1 33.0 1.0 CB A:CYS261 3.1 48.6 1.0 CD2 A:HIS257 3.2 42.9 1.0 CB A:HIS264 3.4 52.4 1.0 NE2 A:HIS264 4.0 45.2 1.0 CD2 A:HIS264 4.1 46.3 1.0 ND1 A:HIS257 4.1 45.1 1.0 N A:HIS264 4.2 53.0 1.0 CG A:HIS257 4.3 46.5 1.0 CA A:HIS264 4.4 55.5 1.0 N A:ASP415 4.5 43.0 1.0 CA A:CYS279 4.5 33.4 1.0 CA A:CYS261 4.6 48.4 1.0 O A:HOH717 4.8 35.0 1.0 CA A:MET276 4.9 44.3 1.0 C A:CYS261 4.9 51.0 1.0 O A:HIS264 5.0 67.8 1.0

Zinc binding site 4 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn607 b:75.5 occ:1.00 OG A:SER112 3.0 42.5 1.0 NE A:ARG278 3.9 38.3 1.0 CB A:SER112 4.0 42.4 1.0 CD A:ARG278 4.0 38.6 1.0 O A:SER112 4.3 39.2 1.0 O A:TRP86 4.3 35.5 1.0 CZ A:ARG278 4.3 37.8 1.0 C A:SER112 4.4 41.3 1.0 CG A:PRO412 4.4 31.2 1.0 CD1 A:ILE87 4.5 38.4 1.0 N A:THR113 4.7 42.9 1.0 NH2 A:ARG278 4.7 38.9 1.0 CG2 A:THR113 4.8 47.3 1.0 NH1 A:ARG278 4.8 37.6 1.0 CA A:SER112 4.9 41.6 1.0 CD A:PRO412 4.9 31.6 1.0 CG2 A:THR173 5.0 30.4 1.0

Zinc binding site 5 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn608 b:88.3 occ:1.00 OH A:TYR494 3.4 50.6 1.0 O A:PRO443 3.5 39.9 1.0 N A:PHE445 3.9 45.3 1.0 CA A:PHE444 3.9 41.0 1.0 O A:PHE445 4.0 47.8 1.0 CE2 A:PHE445 4.0 46.3 1.0 CD2 A:PHE445 4.1 46.7 1.0 CG2 A:VAL316 4.1 51.8 1.0 C A:PHE444 4.3 41.5 1.0 CD1 A:TYR498 4.3 38.8 1.0 C A:PRO443 4.3 40.5 1.0 CE1 A:TYR498 4.4 39.2 1.0 CE2 A:TYR494 4.4 52.6 1.0 CZ A:TYR494 4.4 52.0 1.0 CZ A:PHE445 4.4 45.6 1.0 N A:PHE444 4.5 41.2 1.0 CG A:LEU442 4.5 39.1 1.0 CD1 A:PHE444 4.6 42.1 1.0 CG A:PHE445 4.6 47.1 1.0 CD1 A:LEU508 4.7 38.2 1.0 O A:LEU442 4.8 36.3 1.0 CD1 A:LEU442 4.8 40.1 1.0 CB A:PHE444 4.8 41.3 1.0 C A:PHE445 4.9 51.4 1.0 CA A:PHE445 4.9 48.7 1.0 CE1 A:PHE445 4.9 45.1 1.0 CD2 A:LEU442 5.0 39.3 1.0 CG A:PHE444 5.0 42.4 1.0

Zinc binding site 6 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn805 b:54.7 occ:1.00 SG B:CYS484 2.1 64.6 1.0 SG B:CYS477 2.3 75.6 1.0 ND1 B:HIS487 2.4 77.1 1.0 SG B:CYS452 2.7 85.7 1.0 CB B:CYS452 3.2 83.2 1.0 CB B:CYS484 3.2 71.5 1.0 CE1 B:HIS487 3.2 78.1 1.0 CB B:CYS477 3.3 76.0 1.0 CG B:HIS487 3.4 74.7 1.0 N B:CYS484 3.7 67.4 1.0 CB B:HIS487 3.7 72.5 1.0 CA B:CYS452 3.9 83.9 1.0 CA B:CYS484 4.0 72.2 1.0 NE2 B:HIS487 4.3 76.9 1.0 CD2 B:HIS487 4.4 75.3 1.0 N B:CYS477 4.4 77.1 1.0 CA B:CYS477 4.5 74.8 1.0 CB B:THR475 4.8 68.8 1.0 OG1 B:THR475 4.8 69.5 1.0 O B:CYS484 4.8 83.4 1.0 N B:HIS487 4.8 70.0 1.0 C B:VAL483 4.8 66.7 1.0 C B:CYS484 4.8 76.6 1.0 C B:CYS452 4.8 85.5 1.0 CA B:HIS487 4.9 70.3 1.0 N B:CYS452 4.9 80.9 1.0 O B:PRO451 5.0 82.1 1.0

Zinc binding site 7 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn806 b:64.8 occ:1.00 ND1 B:HIS229 1.8 59.3 1.0 SG B:CYS210 2.2 48.9 1.0 SG B:CYS226 2.3 74.9 1.0 SG B:CYS207 2.4 61.9 1.0 CE1 B:HIS229 2.8 58.0 1.0 CG B:HIS229 2.9 59.3 1.0 CB B:CYS207 3.3 61.9 1.0 CB B:HIS229 3.4 60.1 1.0 CB B:CYS210 3.5 52.2 1.0 CB B:CYS226 3.6 71.9 1.0 N B:CYS210 3.8 55.6 1.0 NE2 B:HIS229 3.9 58.1 1.0 N B:CYS226 3.9 68.4 1.0 CD2 B:HIS229 4.0 59.3 1.0 CA B:CYS210 4.2 53.5 1.0 N B:HIS229 4.3 69.1 1.0 C B:LEU209 4.3 58.1 1.0 CA B:CYS226 4.3 68.6 1.0 CB B:LEU209 4.4 58.6 1.0 CA B:HIS229 4.5 64.5 1.0 N B:LEU209 4.7 61.6 1.0 CB B:ARG212 4.7 60.7 1.0 NH1 B:ARG212 4.7 80.0 1.0 CA B:LEU209 4.7 59.2 1.0 C B:CYS210 4.7 53.2 1.0 CA B:CYS207 4.7 62.3 1.0 O B:CYS210 4.9 52.2 1.0 CB B:HIS228 4.9 68.1 1.0 C B:CYS226 4.9 66.8 1.0 CD B:ARG212 5.0 67.5 1.0 C B:ALA225 5.0 68.6 1.0 O B:LEU209 5.0 56.9 1.0

Zinc binding site 8 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn807 b:59.7 occ:1.00 ND1 B:HIS264 1.9 71.3 1.0 NE2 B:HIS257 2.1 50.6 1.0 SG B:CYS261 2.1 64.9 1.0 SG B:CYS279 2.3 60.4 1.0 CE1 B:HIS264 2.8 71.0 1.0 CE1 B:HIS257 3.0 52.2 1.0 CG B:HIS264 3.0 75.1 1.0 CB B:CYS261 3.1 66.2 1.0 CB B:CYS279 3.2 55.5 1.0 CD2 B:HIS257 3.2 51.7 1.0 CB B:HIS264 3.4 79.9 1.0 NE2 B:HIS264 4.0 71.8 1.0 CD2 B:HIS264 4.1 72.8 1.0 ND1 B:HIS257 4.1 51.5 1.0 O B:HOH918 4.2 31.8 1.0 N B:HIS264 4.2 83.1 1.0 CG1 B:VAL263 4.2 93.7 1.0 CG B:HIS257 4.3 52.5 1.0 CA B:HIS264 4.4 84.6 1.0 N B:ASP415 4.4 55.8 1.0 CA B:CYS261 4.5 68.4 1.0 CA B:CYS279 4.6 54.9 1.0 C B:CYS261 4.9 74.3 1.0 CA B:MET276 4.9 62.4 1.0

Zinc binding site 9 out of 9 in the Structure of NSP14 From Sars-Cov-2 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of NSP14 From Sars-Cov-2 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn808 b:70.1 occ:1.00 OH B:TYR494 3.3 39.8 1.0 O B:PRO443 3.8 39.9 1.0 N B:PHE445 4.0 41.4 1.0 O B:PHE445 4.0 44.7 1.0 CG2 B:VAL316 4.0 46.5 1.0 CA B:PHE444 4.0 38.3 1.0 CE2 B:PHE445 4.1 45.8 1.0 CD2 B:PHE445 4.2 46.3 1.0 CZ B:TYR494 4.3 39.5 1.0 CE2 B:TYR494 4.3 40.2 1.0 CD1 B:TYR498 4.3 43.1 1.0 CE1 B:TYR498 4.3 43.4 1.0 C B:PHE444 4.5 39.2 1.0 CZ B:PHE445 4.6 45.6 1.0 C B:PRO443 4.6 39.7 1.0 CD1 B:LEU508 4.6 41.7 1.0 CD1 B:PHE444 4.6 36.4 1.0 CG B:LEU442 4.6 39.5 1.0 N B:PHE444 4.7 39.0 1.0 CG B:PHE445 4.7 45.7 1.0 C B:PHE445 4.9 44.5 1.0 CG1 B:VAL312 5.0 39.5 1.0 CB B:PHE444 5.0 37.5 1.0 O B:LEU442 5.0 35.9 1.0 CD2 B:LEU442 5.0 39.9 1.0 CA B:PHE445 5.0 43.4 1.0 CD1 B:LEU442 5.0 40.0 1.0

A.Czarna, J.Plewka, L.Kresik, A.Matsuda, A.Karim, C.Robinson, S.O'byrne, F.Cunningham, I.Georgiou, P.Wilk, M.Pachota, G.Popowicz, P.G.Wyatt, G.Dubin, K.Pyrc. Refolding of Lid Subdomain of Sars-Cov-2 NSP14 Upon NSP10 Interaction Releases Exonuclease Activity. Structure V. 30 1050 2022.
ISSN: ISSN 0969-2126
PubMed: 35609600
DOI: 10.1016/J.STR.2022.04.014