Zinc in PDB 7orr: Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00022

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00022, PDB code: 7orr 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)	53.00 / 1.79
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	105.883, 105.883, 105.883, 90, 90, 90
R / Rfree (%)	17.2 / 18.4

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00022 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 VT00022 (pdb code 7orr). 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 VT00022, PDB code: 7orr:
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 VT00022


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 VT00022 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:36.7 occ:1.00 NE2 A:HIS83 2.1 35.2 1.0 SG A:CYS74 2.3 35.2 1.0 SG A:CYS77 2.3 38.5 1.0 SG A:CYS90 2.3 40.2 1.0 CD2 A:HIS83 3.0 36.4 1.0 CE1 A:HIS83 3.1 39.6 1.0 CB A:CYS74 3.2 32.5 1.0 CB A:CYS90 3.3 42.9 1.0 CB A:CYS77 3.4 34.3 1.0 N A:CYS77 3.6 33.5 1.0 CA A:CYS77 4.0 34.3 1.0 ND1 A:HIS83 4.2 39.7 1.0 CG A:HIS83 4.2 38.6 1.0 O A:HOH376 4.3 48.3 1.0 CA A:CYS90 4.5 43.8 1.0 CB A:TYR76 4.5 34.2 1.0 C A:TYR76 4.5 32.8 1.0 O A:HOH372 4.6 57.7 1.0 CA A:CYS74 4.6 31.2 1.0 CB A:LYS93 4.9 48.0 1.0 CA A:TYR76 4.9 33.3 1.0 O A:CYS74 4.9 31.1 1.0 C A:CYS74 4.9 31.6 1.0 N A:LYS93 5.0 39.6 1.0 N A:TYR76 5.0 32.0 1.0

Zinc binding site 2 out of 2 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00022


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 VT00022 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:67.8 occ:1.00 SG A:CYS117 2.1 56.3 1.0 SG A:CYS128 2.2 68.0 1.0 SG A:CYS120 2.3 64.8 1.0 SG A:CYS130 2.7 83.9 1.0 CB A:CYS117 3.0 61.6 1.0 CB A:CYS128 3.4 68.6 1.0 CB A:CYS120 3.4 65.0 1.0 CB A:CYS130 3.4 81.9 1.0 N A:CYS120 3.8 66.4 1.0 CA A:CYS128 4.0 70.6 1.0 CA A:CYS120 4.2 64.4 1.0 N A:CYS130 4.2 83.5 1.0 CA A:CYS130 4.4 84.7 1.0 CA A:CYS117 4.5 60.3 1.0 CB A:VAL119 4.6 77.3 1.0 N A:SER129 4.6 84.4 1.0 C A:CYS128 4.6 78.3 1.0 C A:VAL119 4.9 71.7 1.0 C A:CYS120 5.0 59.8 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