Chlorine in PDB 5r83: Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329, PDB code: 5r83 was solved by D.Fearon, A.J.Powell, A.Douangamath, C.D.Owen, C.Wild, T.Krojer, P.Lukacik, C.M.Strain-Damerell, M.A.Walsh, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.71 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.709, 52.583, 111.114, 90.00, 159.75, 90.00
R / Rfree (%)	23.3 / 26.5

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329 (pdb code 5r83). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329, PDB code: 5r83:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1005 b:38.8 occ:1.00 OD2 A:ASP187 2.7 21.6 1.0 ND1 A:HIS164 2.9 20.4 1.0 N A:HIS41 3.1 21.9 1.0 ND1 A:HIS41 3.2 26.4 1.0 N A:ARG40 3.4 19.4 1.0 CE1 A:HIS164 3.5 20.1 1.0 CB A:ASP187 3.5 22.8 1.0 CB A:HIS41 3.5 23.3 1.0 CG A:ASP187 3.5 23.0 1.0 O A:CYS85 3.5 20.2 1.0 CG A:ARG40 3.6 18.9 1.0 CG A:HIS41 3.7 23.9 1.0 CB A:PRO39 3.8 19.9 1.0 CA A:HIS41 3.9 23.5 1.0 C A:PRO39 3.9 20.1 1.0 C A:ARG40 4.0 19.2 1.0 CA A:PRO39 4.0 19.6 1.0 CA A:ARG40 4.1 19.6 1.0 CG A:HIS164 4.1 19.4 1.0 CE1 A:HIS41 4.2 23.3 1.0 CB A:ARG40 4.4 20.0 1.0 OH A:TYR54 4.4 24.7 1.0 CB A:CYS85 4.5 19.6 1.0 C A:CYS85 4.6 20.1 1.0 CB A:HIS164 4.6 19.5 1.0 NE A:ARG40 4.7 20.3 1.0 CD A:ARG40 4.7 19.4 1.0 NE2 A:HIS164 4.8 21.6 1.0 OD1 A:ASP187 4.8 23.0 1.0 CD2 A:HIS41 4.8 25.6 1.0 O A:PRO39 4.8 21.5 1.0 CZ A:TYR54 4.9 24.6 1.0 CA A:ASP187 4.9 23.6 1.0 CA A:CYS85 5.0 18.0 1.0

Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1006 b:69.2 occ:1.00 NH2 A:ARG40 3.8 23.1 1.0 O A:HOH1180 4.1 34.9 1.0 O A:HOH1172 4.1 37.8 1.0 SG A:CYS85 4.2 20.6 1.0 O A:HOH1141 4.4 29.9 1.0 CZ A:ARG40 4.5 22.4 1.0 NH1 A:ARG40 4.5 21.5 1.0 O A:HOH1153 4.7 24.5 1.0 C A:ASN84 4.9 20.2 1.0 CA A:ASN84 4.9 21.6 1.0

Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1007 b:39.9 occ:1.00 O A:LEU115 2.6 19.6 1.0 N A:VAL148 2.9 20.0 1.0 SD A:MET17 3.2 23.7 1.0 CG2 A:VAL148 3.4 19.7 1.0 CB A:LEU115 3.5 21.6 1.0 CA A:SER147 3.5 19.8 1.0 CE A:MET17 3.5 25.8 1.0 C A:LEU115 3.6 21.1 1.0 C A:SER147 3.6 19.7 1.0 SG A:CYS117 3.7 25.4 1.0 CA A:VAL148 3.9 19.2 1.0 O A:VAL148 3.9 20.1 1.0 CA A:LEU115 4.0 20.0 1.0 CG A:LEU115 4.0 22.6 1.0 CB A:SER147 4.0 20.3 1.0 CG A:MET17 4.1 21.4 1.0 CB A:VAL148 4.1 20.8 1.0 CD2 A:LEU115 4.2 22.1 1.0 N A:LEU115 4.3 19.9 1.0 CG1 A:VAL13 4.3 19.6 1.0 C A:VAL148 4.3 22.3 1.0 OG A:SER147 4.5 21.5 1.0 CG1 A:VAL148 4.6 19.7 1.0 O A:GLY146 4.7 21.9 1.0 CB A:CYS117 4.7 24.3 1.0 N A:SER147 4.7 21.3 1.0 N A:ALA116 4.8 21.4 1.0 O A:SER147 4.9 18.7 1.0

Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1008 b:43.7 occ:1.00 N A:GLY195 2.7 24.7 1.0 O A:ASN133 2.8 21.0 1.0 CA A:ALA194 3.2 32.7 1.0 O A:HOH1126 3.3 52.8 1.0 CB A:ASN133 3.4 22.0 1.0 CZ A:PHE185 3.4 23.3 1.0 C A:ALA194 3.4 30.8 1.0 CB A:ALA194 3.7 32.4 1.0 C A:ASN133 3.7 22.2 1.0 CA A:GLY195 3.7 23.8 1.0 CA A:ASN133 3.9 22.5 1.0 CG A:ASN133 3.9 21.2 1.0 CE2 A:PHE185 4.1 23.5 1.0 ND2 A:ASN133 4.3 20.5 1.0 CE1 A:PHE185 4.3 22.6 1.0 O A:ALA193 4.4 32.3 1.0 N A:ALA194 4.5 30.9 1.0 CG2 A:THR135 4.5 21.4 1.0 OD1 A:ASN133 4.5 21.6 1.0 C A:GLY195 4.6 22.6 1.0 O A:GLY195 4.6 18.9 1.0 O A:ALA194 4.6 33.2 1.0 CD A:PRO184 4.7 25.0 1.0 CG A:PRO184 4.8 24.7 1.0 C A:ALA193 4.9 33.1 1.0 N A:PHE134 5.0 23.2 1.0

Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1009 b:51.8 occ:1.00 O A:THR224 2.8 24.9 1.0 O A:HOH1127 2.8 39.7 1.0 NZ A:LYS269 3.3 35.6 1.0 CB A:THR225 3.8 24.4 1.0 C A:THR224 3.8 23.5 1.0 CD A:LYS269 3.8 31.9 1.0 CE A:LYS269 4.0 34.1 1.0 CB A:ALA266 4.0 23.4 1.0 CB A:PHE223 4.1 33.9 1.0 OD2 A:ASP229 4.2 40.6 1.0 CA A:THR225 4.2 22.7 1.0 OG1 A:THR225 4.3 25.9 1.0 N A:THR225 4.4 23.4 1.0 CA A:ALA266 4.6 22.4 1.0 OE2 A:GLU270 4.7 37.5 1.0 N A:THR224 4.7 24.2 1.0 CG2 A:THR225 4.9 24.7 1.0 CA A:THR224 4.9 23.6 1.0 CG A:PHE223 4.9 34.8 1.0 CL A:CL1010 4.9 43.1 1.0 CG A:LYS269 5.0 29.6 1.0

Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of Covid-19 Main Protease in Complex with Z44592329 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1010 b:43.1 occ:1.00 N A:THR224 2.9 24.2 1.0 CA A:PHE223 3.3 30.0 1.0 O A:THR224 3.5 24.9 1.0 C A:PHE223 3.6 27.5 1.0 CB A:PHE223 3.6 33.9 1.0 CA A:THR224 4.0 23.6 1.0 C A:THR224 4.1 23.5 1.0 CG2 A:THR224 4.2 24.1 1.0 O A:ARG222 4.4 32.8 1.0 CD1 A:PHE223 4.4 38.1 1.0 CG A:PHE223 4.4 34.8 1.0 CB A:THR224 4.5 23.9 1.0 N A:PHE223 4.6 32.0 1.0 O A:PHE223 4.8 22.7 1.0 C A:ARG222 4.9 34.6 1.0 CL A:CL1009 4.9 51.8 1.0

D.Fearon, A.J.Powell, A.Douangamath, C.D.Owen, C.Wild, T.Krojer, P.Lukacik, C.M.Strain-Damerell, M.A.Walsh, F.Von Delft. Pandda Analysis of Covid-19 Main Protease Against the Dsi-Poised Fragment Library To Be Published.