Zinc in PDB 7oru: Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221, PDB code: 7oru was solved by V.O.Talibov, F.Kozielski, C.Sele, J.Lou, D.Dong, Q.Wang, X.Shi, M.Nyblom, A.Rogstam, T.Krojer, W.Knecht, S.Z.Fisher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.78 / 1.67
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	106.775, 106.775, 106.775, 90, 90, 90
R / Rfree (%)	16.1 / 17.2

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221 (pdb code 7oru). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221, PDB code: 7oru:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:28.5 occ:1.00 NE2 A:HIS83 2.1 28.5 1.0 SG A:CYS77 2.3 29.3 1.0 SG A:CYS74 2.3 27.0 1.0 SG A:CYS90 2.3 30.6 1.0 CD2 A:HIS83 3.0 29.9 1.0 CE1 A:HIS83 3.1 32.2 1.0 CB A:CYS74 3.2 26.2 1.0 CB A:CYS90 3.3 31.6 1.0 CB A:CYS77 3.4 27.0 1.0 N A:CYS77 3.6 25.0 1.0 CA A:CYS77 4.0 26.2 1.0 CG A:HIS83 4.2 30.2 1.0 ND1 A:HIS83 4.2 31.0 1.0 O A:HOH394 4.5 42.7 1.0 CA A:CYS90 4.5 33.6 1.0 CB A:TYR76 4.5 26.8 1.0 C A:TYR76 4.5 24.8 1.0 O A:HOH447 4.6 47.3 1.0 CA A:CYS74 4.6 25.5 1.0 CA A:TYR76 4.9 26.1 1.0 CB A:LYS93 4.9 37.7 1.0 C A:CYS74 5.0 25.3 1.0 N A:LYS93 5.0 31.1 1.0 N A:TYR76 5.0 24.7 1.0

Zinc binding site 2 out of 2 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:49.6 occ:1.00 SG A:CYS117 2.2 46.7 1.0 SG A:CYS128 2.2 51.4 1.0 SG A:CYS120 2.4 44.3 1.0 SG A:CYS130 2.4 61.1 1.0 CB A:CYS117 3.1 45.6 1.0 CB A:CYS130 3.2 65.7 1.0 CB A:CYS128 3.4 52.7 1.0 CB A:CYS120 3.4 45.1 1.0 N A:CYS120 3.9 47.9 1.0 N A:CYS130 3.9 67.9 1.0 CA A:CYS128 4.0 51.6 1.0 CA A:CYS130 4.1 67.5 1.0 CA A:CYS120 4.2 45.9 1.0 N A:SER129 4.3 64.1 1.0 C A:CYS128 4.5 57.1 1.0 CA A:CYS117 4.5 43.7 1.0 CB A:VAL119 4.5 58.4 1.0 C A:CYS120 5.0 41.9 1.0 C A:VAL119 5.0 53.7 1.0 C A:SER129 5.0 69.6 1.0

F.Kozielski, C.Sele, V.O.Talibov, J.Lou, D.Dong, Q.Wang, X.Shi, M.Nyblom, A.Rogstam, T.Krojer, Z.Fisher, W.Knecht. Identification of Fragments Binding to Sars-Cov-2 NSP10 Reveals Ligand-Binding Sites in Conserved Interfaces Between NSP10 and NSP14/NSP16 Rsc Chem Biol 2021.
ISSN: ESSN 2633-0679
DOI: 10.1039/D1CB00135C