Chlorine in PDB 7orv: Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239, PDB code: 7orv 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)	28.66 / 1.95
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	107.236, 107.236, 107.236, 90, 90, 90
R / Rfree (%)	17 / 20.2

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Chlorine atom in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 (pdb code 7orv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239, PDB code: 7orv:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl207 b:48.0 occ:1.00 O A:HOH330 3.1 38.2 1.0 O A:HOH367 3.2 51.6 1.0 N A:VAL21 3.4 45.9 1.0 CA A:ALA20 3.8 42.5 1.0 C A:ALA20 4.1 44.2 1.0 CG2 A:VAL21 4.2 48.1 1.0 CB A:ALA20 4.2 45.7 1.0 CB A:VAL21 4.3 52.0 1.0 O2 A:GOL206 4.4 67.2 1.0 CA A:VAL21 4.4 47.0 1.0 O1 A:GOL206 4.7 64.8 1.0 O A:PHE19 4.8 42.0 1.0 C1 A:GOL206 4.9 73.8 1.0 N A:ALA20 4.9 40.5 1.0

Chlorine binding site 2 out of 3 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl208 b:63.9 occ:1.00 O A:HOH382 2.8 57.1 1.0 O A:HOH349 3.2 51.6 1.0 N A:GLY127 3.2 61.3 1.0 NE2 A:GLN65 3.2 49.1 1.0 CA A:GLY127 3.5 65.1 1.0 CB A:TYR126 3.8 54.9 1.0 CD1 A:TRP123 3.8 47.7 1.0 CG A:PRO100 3.8 50.8 1.0 CB A:TRP123 4.1 51.8 1.0 CD A:PRO100 4.1 49.2 1.0 C A:TYR126 4.2 63.7 1.0 CD A:GLN65 4.3 44.0 1.0 CG A:TRP123 4.4 48.3 1.0 O A:HOH359 4.4 59.0 1.0 CG A:GLN65 4.4 46.3 1.0 N A:TRP123 4.6 53.9 1.0 CA A:TYR126 4.6 59.0 1.0 CB A:PRO100 4.8 49.7 1.0 N A:PRO100 4.8 45.7 1.0 O A:GLY52 4.8 45.9 1.0 CG A:TYR126 4.9 51.2 1.0 CA A:TRP123 4.9 52.9 1.0 O A:TRP123 4.9 58.5 1.0 C A:GLY127 5.0 67.6 1.0

Chlorine binding site 3 out of 3 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl209 b:55.6 occ:1.00 O A:HOH370 2.8 61.0 1.0 OG1 A:THR12 3.1 41.7 1.0 O A:HOH374 3.3 45.5 1.0 N A:THR12 3.3 39.0 1.0 O A:MET8 3.5 50.7 1.0 CA A:GLY9 3.5 46.0 1.0 C A:GLY9 3.7 41.2 1.0 N A:SER11 3.7 40.6 1.0 CB A:SER11 3.8 41.0 1.0 CB A:THR12 3.9 40.0 1.0 O A:GLY9 3.9 41.3 1.0 CA A:SER11 4.0 39.2 1.0 C A:SER11 4.1 41.4 1.0 N A:ASN10 4.2 39.7 1.0 CA A:THR12 4.2 39.0 1.0 C A:MET8 4.3 51.2 1.0 N A:GLY9 4.4 46.6 1.0 C A:ASN10 4.6 37.4 1.0 OG A:SER11 4.7 41.9 1.0 O A:HOH338 4.8 55.1 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