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Chlorine in PDB 7gly: Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057)

Enzymatic activity of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057)

All present enzymatic activity of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057):
3.4.22.69;

Protein crystallography data

The structure of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057), PDB code: 7gly was solved by D.Fearon, A.Aimon, J.C.Aschenbrenner, B.H.Balcomb, F.K.R.Bertram, J.Brandao-Neto, A.Dias, A.Douangamath, L.Dunnett, A.S.Godoy, T.J.Gorrie-Stone, L.Koekemoer, T.Krojer, R.M.Lithgo, P.Lukacik, P.G.Marples, H.Mikolajek, E.Nelson, C.D.Owen, A.J.Powell, V.L.Rangel, R.Skyner, C.M.Strain-Damerell, W.Thompson, C.W.E.Tomlinson, C.Wild, 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) 34.03 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.055, 100.646, 104.66, 90, 90, 90
R / Rfree (%) 21.4 / 24.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057) (pdb code 7gly). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057), PDB code: 7gly:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gly

Go back to Chlorine Binding Sites List in 7gly
Chlorine binding site 1 out of 3 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:25.0
occ:1.00
 NE2 A:GLN110 3.1 26.5 1.0
N A:GLN107 3.3 22.7 1.0
CA A:ILE106 3.7 21.4 1.0
CG A:GLN110 3.8 21.4 1.0
CB A:GLN110 3.8 19.9 1.0
CD A:GLN110 3.9 24.7 1.0
CB A:ILE106 4.0 20.9 1.0
C A:ILE106 4.0 22.6 1.0
CB A:GLN107 4.0 24.8 1.0
CG A:GLN107 4.1 29.5 1.0
CA A:GLN107 4.2 23.5 1.0
CG2 A:ILE106 4.3 20.7 1.0
O A:GLN107 4.5 23.6 1.0
O A:HOH678 4.8 29.9 1.0
O A:ARG105 4.8 21.8 1.0
C A:GLN107 4.9 24.0 1.0

Chlorine binding site 2 out of 3 in 7gly

Go back to Chlorine Binding Sites List in 7gly
Chlorine binding site 2 out of 3 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:30.1
occ:0.86
 CL A:RDX407 0.0 30.1 0.9
C17 A:RDX407 1.7 30.7 0.9
C18 A:RDX407 2.7 31.0 0.9
C16 A:RDX407 2.7 30.9 0.9
CD2 A:HIS41 3.6 30.0 1.0
CB A:ASP187 3.6 29.4 1.0
CA A:ASP187 3.6 29.1 1.0
O A:HIS164 3.7 21.8 1.0
CB A:MET165 3.8 23.8 1.0
SD A:MET165 3.9 36.1 1.0
C19 A:RDX407 4.0 31.6 0.9
CE A:MET49 4.0 47.4 1.0
C15 A:RDX407 4.0 31.4 0.9
NE2 A:HIS41 4.1 31.0 1.0
C A:ASP187 4.1 30.2 1.0
CG A:HIS41 4.2 28.3 1.0
C A:HIS164 4.3 21.1 1.0
CG A:MET165 4.3 27.3 1.0
N A:ARG188 4.4 31.4 1.0
CB A:HIS164 4.5 19.1 1.0
C20 A:RDX407 4.5 32.4 0.9
CB A:HIS41 4.6 25.3 1.0
O A:HOH528 4.6 15.9 1.0
CA A:MET165 4.8 22.3 1.0
O A:ASP187 4.8 30.3 1.0
CE1 A:HIS41 4.8 30.7 1.0
N A:MET165 4.8 20.9 1.0
N A:ASP187 4.9 28.9 1.0
ND1 A:HIS41 4.9 30.4 1.0
O A:VAL186 4.9 29.5 1.0
CA A:HIS164 4.9 19.8 1.0
CD2 A:HIS164 5.0 17.3 1.0

Chlorine binding site 3 out of 3 in 7gly

Go back to Chlorine Binding Sites List in 7gly
Chlorine binding site 3 out of 3 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-5CD9EA36-23 (Mpro-P2057) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:27.4
occ:0.76
 CL B:RDX405 0.0 27.4 0.8
C17 B:RDX405 1.7 28.1 0.8
C18 B:RDX405 2.7 28.5 0.8
C16 B:RDX405 2.7 28.8 0.8
CB B:ASP187 3.5 32.3 1.0
CA B:ASP187 3.5 31.6 1.0
CD2 B:HIS41 3.7 37.2 1.0
CB B:MET165 3.7 28.6 1.0
C B:ASP187 3.9 35.4 1.0
O B:HIS164 3.9 24.9 1.0
SD B:MET165 4.0 47.1 1.0
C19 B:RDX405 4.0 29.2 0.8
C15 B:RDX405 4.0 29.4 0.8
N B:ARG188 4.1 37.0 1.0
CG B:MET165 4.2 33.6 1.0
NE2 B:HIS41 4.2 38.7 1.0
CG B:HIS41 4.3 36.1 1.0
C B:HIS164 4.3 24.5 1.0
CB B:HIS164 4.4 23.2 1.0
CE B:MET49 4.5 76.2 1.0
O B:ASP187 4.5 36.3 1.0
C20 B:RDX405 4.5 30.0 0.8
O B:HOH526 4.6 18.7 1.0
CB B:HIS41 4.7 32.7 1.0
CA B:MET165 4.8 26.6 1.0
N B:MET165 4.8 25.1 1.0
O B:VAL186 4.8 28.3 1.0
N B:ASP187 4.8 29.3 1.0
CE1 B:HIS41 4.9 39.1 1.0
CA B:HIS164 4.9 23.0 1.0
CG B:ASP187 4.9 33.7 1.0
CZ B:PHE181 5.0 22.7 1.0

Reference:

M.L.Boby, D.Fearon, M.Ferla, M.Filep, L.Koekemoer, M.C.Robinson, The Covid Moonshot Consortium, J.D.Chodera, A.A.Lee, N.London, A.Von Delft, F.Von Delft. Open Science Discovery of Potent Noncovalent Sars-Cov-2 Main Protease Inhibitors Science 2023.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABO7201
Page generated: Sun Jul 13 01:52:54 2025

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