Zinc in PDB 7diy: Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain

The structure of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain, PDB code: 7diy was solved by S.Lin, H.Chen, Z.M.Chen, F.L.Yang, F.Ye, Y.Zheng, J.Yang, X.Lin, H.L.Sun, L.L.Wang, A.Wen, Y.Cao, G.W.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.77 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.929, 68.28, 109.739, 90, 90, 90
R / Rfree (%)	23 / 26.4

The structure of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain (pdb code 7diy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain, PDB code: 7diy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:36.9 occ:1.00 SG A:CYS90 2.1 37.9 1.0 SG A:CYS74 2.2 37.0 1.0 SG A:CYS77 2.3 36.5 1.0 NE2 A:HIS83 2.4 36.7 1.0 CB A:CYS74 3.0 37.0 1.0 CD2 A:HIS83 3.1 37.1 1.0 CB A:CYS90 3.2 38.2 1.0 CB A:CYS77 3.2 36.0 1.0 N A:CYS77 3.3 35.7 1.0 CE1 A:HIS83 3.5 36.5 1.0 CA A:CYS77 3.8 35.6 1.0 CA A:CYS90 4.2 38.7 1.0 C A:TYR76 4.3 35.4 1.0 CG A:HIS83 4.3 37.0 1.0 CB A:TYR76 4.4 35.9 1.0 CA A:CYS74 4.4 36.9 1.0 ND1 A:HIS83 4.5 36.7 1.0 CA A:TYR76 4.7 35.5 1.0 O A:CYS74 4.7 36.0 1.0 N A:TYR76 4.8 35.7 1.0 C A:CYS74 4.8 36.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:52.4 occ:1.00 SG A:CYS128 1.8 56.0 1.0 SG A:CYS117 2.3 51.8 1.0 SG A:CYS130 2.3 54.8 1.0 SG A:CYS120 2.5 51.9 1.0 CB A:CYS117 2.7 50.3 1.0 CB A:CYS128 3.1 51.4 1.0 CB A:CYS120 3.5 52.8 1.0 N A:CYS120 3.9 52.3 1.0 CA A:CYS128 4.0 51.9 1.0 CB A:CYS130 4.1 56.8 1.0 CA A:CYS117 4.2 49.3 1.0 N A:CYS130 4.2 56.3 1.0 CA A:CYS120 4.2 52.1 1.0 N A:SER129 4.5 54.3 1.0 C A:CYS128 4.5 53.4 1.0 O A:CYS130 4.6 58.3 1.0 CA A:CYS130 4.7 57.4 1.0 N A:GLY121 4.7 49.8 1.0 C A:CYS120 4.7 50.7 1.0 CB A:VAL119 4.8 54.5 1.0 C A:CYS117 4.8 49.3 1.0 O A:MET122 4.9 47.9 1.0 N A:CYS117 5.0 48.0 1.0 O A:CYS117 5.0 49.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:38.4 occ:1.00 ND1 B:HIS229 2.2 38.6 1.0 SG B:CYS210 2.2 39.4 1.0 SG B:CYS207 2.2 38.2 1.0 SG B:CYS226 2.2 37.5 1.0 CE1 B:HIS229 2.8 39.1 1.0 CB B:CYS210 2.9 39.7 1.0 CB B:CYS226 3.2 37.0 1.0 CB B:CYS207 3.3 38.1 1.0 CG B:HIS229 3.3 38.7 1.0 N B:CYS226 3.8 36.7 1.0 CB B:HIS229 3.9 38.2 1.0 NE2 B:HIS229 4.0 39.6 1.0 CA B:CYS226 4.1 36.4 1.0 CA B:CYS210 4.2 40.6 1.0 CD2 B:HIS229 4.3 39.3 1.0 O B:LEU209 4.3 41.0 1.0 O B:CYS208 4.4 42.2 1.0 NH1 B:ARG212 4.5 39.0 1.0 C B:LEU209 4.5 40.9 1.0 N B:CYS210 4.5 40.8 1.0 CB B:ARG212 4.6 38.4 1.0 N B:HIS229 4.6 37.3 1.0 CA B:CYS207 4.7 38.3 1.0 CD B:ARG212 4.8 38.4 1.0 CB B:LEU209 4.8 40.5 1.0 C B:CYS226 4.9 36.1 1.0 CA B:HIS229 4.9 37.7 1.0 C B:ALA225 5.0 36.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:40.8 occ:1.00 ND1 B:HIS264 2.0 40.4 1.0 SG B:CYS279 2.1 40.3 1.0 NE2 B:HIS257 2.2 41.1 1.0 SG B:CYS261 2.2 42.3 1.0 CE1 B:HIS264 2.9 39.9 1.0 CB B:CYS261 3.0 42.8 1.0 CE1 B:HIS257 3.1 41.8 1.0 CG B:HIS264 3.1 40.5 1.0 CB B:CYS279 3.1 39.2 1.0 CD2 B:HIS257 3.2 40.8 1.0 CB B:HIS264 3.6 41.0 1.0 NE2 B:HIS264 4.1 39.7 1.0 CD2 B:HIS264 4.2 40.1 1.0 ND1 B:HIS257 4.2 41.9 1.0 CG B:HIS257 4.3 41.3 1.0 CA B:CYS261 4.4 43.9 1.0 CA B:CYS279 4.6 38.8 1.0 N B:HIS264 4.6 42.6 1.0 CA B:HIS264 4.7 41.8 1.0 CG2 B:VAL263 4.8 42.8 1.0 C B:CYS261 4.9 44.4 1.0 CE1 B:HIS283 4.9 42.0 1.0

S.Lin, H.Chen, Z.Chen, F.Yang, F.Ye, Y.Zheng, J.Yang, X.Lin, H.Sun, L.Wang, A.Wen, H.Dong, Q.Xiao, D.Deng, Y.Cao, G.Lu. Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exon Domain Reveals An Exoribonuclease with Both Structural and Functional Integrity. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33956156
DOI: 10.1093/NAR/GKAB320