Zinc in PDB 9fw2: Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14

The structure of Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14, PDB code: 9fw2 was solved by S.Z.Fisher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.98 / 1.77
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.029, 104.782, 55.124, 90, 90, 90
R / Rfree (%)	16.7 / 18.3

The structure of Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14 (pdb code 9fw2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14, PDB code: 9fw2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:23.2 occ:0.94 SG A:CYS120 2.3 21.6 1.0 SG A:CYS130 2.3 26.1 1.0 SG A:CYS128 2.4 23.1 1.0 SG A:CYS117 2.4 24.3 1.0 CB A:CYS117 3.1 20.2 1.0 CB A:CYS130 3.2 30.4 1.0 CB A:CYS120 3.3 21.0 1.0 CB A:CYS128 3.4 18.1 1.0 N A:CYS120 3.8 23.4 1.0 N A:CYS130 3.9 30.0 1.0 CA A:CYS128 4.1 24.5 1.0 O A:HOH307 4.1 26.9 1.0 CA A:CYS120 4.2 21.8 1.0 CA A:CYS130 4.2 32.0 1.0 N A:SER129 4.4 25.0 1.0 C A:CYS128 4.5 28.3 1.0 CA A:CYS117 4.6 21.6 1.0 O A:HOH429 4.6 35.6 1.0 CB A:VAL119 4.6 31.4 1.0 C A:VAL119 4.9 29.7 1.0 C A:CYS120 4.9 25.4 1.0

Zinc binding site 2 out of 4 in the Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:17.6 occ:1.00 SG A:CYS74 2.3 16.6 1.0 SG A:CYS77 2.3 17.5 1.0 SG A:CYS90 2.3 18.1 1.0 NE2 A:HIS83 2.5 26.0 1.0 CB A:CYS90 3.1 18.3 1.0 CB A:CYS74 3.2 16.4 1.0 CD2 A:HIS83 3.3 21.5 1.0 CB A:CYS77 3.5 14.5 1.0 N A:CYS77 3.6 15.2 1.0 CE1 A:HIS83 3.6 18.6 1.0 CA A:CYS77 4.0 14.5 1.0 CA A:CYS90 4.4 20.0 1.0 O A:HOH468 4.4 26.3 1.0 C A:TYR76 4.5 17.8 1.0 CB A:TYR76 4.5 13.4 1.0 O A:HOH334 4.5 21.7 1.0 CG A:HIS83 4.5 21.4 1.0 CA A:CYS74 4.6 14.3 1.0 ND1 A:HIS83 4.6 23.7 1.0 CB A:LYS93 4.8 14.6 1.0 N A:LYS93 4.9 17.6 1.0 CA A:TYR76 4.9 15.1 1.0 C A:CYS74 4.9 15.4 1.0 O A:CYS74 4.9 15.0 1.0 N A:TYR76 4.9 14.9 1.0

Zinc binding site 3 out of 4 in the Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.8 occ:1.00 ND1 B:HIS264 2.0 16.7 1.0 NE2 B:HIS257 2.1 17.4 1.0 SG B:CYS279 2.3 19.6 1.0 SG B:CYS261 2.4 21.2 1.0 CE1 B:HIS264 2.9 18.3 1.0 CE1 B:HIS257 3.0 21.7 1.0 CD2 B:HIS257 3.0 16.3 1.0 CB B:CYS261 3.0 16.5 1.0 CG B:HIS264 3.1 21.2 1.0 CB B:CYS279 3.3 18.5 1.0 CB B:HIS264 3.5 20.9 1.0 NE2 B:HIS264 4.0 16.6 1.0 ND1 B:HIS257 4.1 21.1 1.0 CG B:HIS257 4.1 18.6 1.0 O B:HOH694 4.1 25.0 1.0 CD2 B:HIS264 4.1 18.8 1.0 O B:HOH749 4.2 27.1 1.0 O B:HOH625 4.4 21.4 1.0 N B:HIS264 4.5 24.4 1.0 CA B:CYS261 4.5 26.5 1.0 CA B:HIS264 4.6 24.2 1.0 CA B:CYS279 4.7 15.4 1.0 C B:CYS261 4.9 28.7 1.0 CG2 B:VAL263 4.9 23.4 1.0 CE1 B:HIS283 5.0 25.1 1.0

Zinc binding site 4 out of 4 in the Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars Cov-2 NSP10 in Complex with the Exon Domain From NSP14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.9 occ:1.00 ND1 B:HIS229 2.2 18.8 1.0 SG B:CYS207 2.3 17.2 1.0 SG B:CYS210 2.3 18.1 1.0 SG B:CYS226 2.3 16.2 1.0 CE1 B:HIS229 3.0 22.3 1.0 CB B:CYS207 3.1 10.6 1.0 CG B:HIS229 3.3 18.5 1.0 CB B:CYS226 3.5 13.8 1.0 CB B:CYS210 3.5 20.1 1.0 CB B:HIS229 3.7 19.5 1.0 N B:CYS210 3.9 17.9 1.0 N B:CYS226 4.0 14.7 1.0 NE2 B:HIS229 4.2 21.3 1.0 CA B:CYS210 4.2 17.6 1.0 CA B:CYS226 4.3 13.7 1.0 CD2 B:HIS229 4.4 21.5 1.0 C B:LEU209 4.4 18.1 1.0 NH1 B:ARG212 4.4 21.9 1.0 N B:HIS229 4.5 17.6 1.0 CB B:LEU209 4.5 19.3 1.0 CA B:CYS207 4.6 14.3 1.0 C B:CYS210 4.7 14.4 1.0 N B:LEU209 4.7 17.6 1.0 CA B:LEU209 4.8 15.3 1.0 CB B:ARG212 4.8 14.9 1.0 CA B:HIS229 4.8 16.4 1.0 CB B:HIS228 4.8 16.7 1.0 CD B:ARG212 4.8 17.5 1.0 C B:CYS226 4.9 14.9 1.0 O B:CYS210 4.9 18.4 1.0

S.Z.Fisher, S.Z.Fisher. N/A N/A.