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Chlorine in PDB 7gm4: 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 Alp-Pos-6F6AE286-5 (Mpro-P2080)

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 Alp-Pos-6F6AE286-5 (Mpro-P2080)

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 Alp-Pos-6F6AE286-5 (Mpro-P2080):
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 Alp-Pos-6F6AE286-5 (Mpro-P2080), PDB code: 7gm4 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) 33.97 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.946, 100.546, 104.545, 90, 90, 90
R / Rfree (%) 23 / 26.4

Other elements in 7gm4:

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 Alp-Pos-6F6AE286-5 (Mpro-P2080) also contains other interesting chemical elements:

Fluorine (F) 2 atoms

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 Alp-Pos-6F6AE286-5 (Mpro-P2080) (pdb code 7gm4). 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 Alp-Pos-6F6AE286-5 (Mpro-P2080), PDB code: 7gm4:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gm4

Go back to Chlorine Binding Sites List in 7gm4
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 Alp-Pos-6F6AE286-5 (Mpro-P2080)


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 Alp-Pos-6F6AE286-5 (Mpro-P2080) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:19.4
occ:1.00
 NE2 A:GLN110 3.1 20.8 1.0
N A:GLN107 3.2 17.7 1.0
CA A:ILE106 3.7 15.6 1.0
CG A:GLN110 3.7 16.9 1.0
CB A:GLN110 3.7 14.8 1.0
CD A:GLN110 3.9 21.0 1.0
CB A:ILE106 3.9 15.0 1.0
C A:ILE106 3.9 17.0 1.0
CB A:GLN107 4.0 20.1 1.0
CG A:GLN107 4.1 23.3 1.0
CA A:GLN107 4.2 19.1 1.0
CG2 A:ILE106 4.2 14.3 1.0
O A:GLN107 4.5 20.4 1.0
O A:HOH660 4.7 21.1 1.0
O A:ARG105 4.8 16.8 1.0
C A:GLN107 4.8 20.0 1.0

Chlorine binding site 2 out of 3 in 7gm4

Go back to Chlorine Binding Sites List in 7gm4
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 Alp-Pos-6F6AE286-5 (Mpro-P2080)


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 Alp-Pos-6F6AE286-5 (Mpro-P2080) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:30.5
occ:0.94
 CL A:RGQ407 0.0 30.5 0.9
C17 A:RGQ407 1.7 30.9 0.9
C18 A:RGQ407 2.7 31.3 0.9
C16 A:RGQ407 2.7 31.1 0.9
CD2 A:HIS41 3.5 26.1 1.0
CA A:ASP187 3.6 27.1 1.0
CB A:ASP187 3.6 26.9 1.0
O A:HIS164 3.6 21.9 1.0
CB A:MET165 3.7 24.1 1.0
SD A:MET165 3.9 34.8 1.0
CE A:MET49 4.0 42.0 1.0
C A:ASP187 4.0 28.1 1.0
C19 A:RGQ407 4.0 31.7 0.9
C15 A:RGQ407 4.0 31.3 0.9
NE2 A:HIS41 4.0 27.2 1.0
CG A:HIS41 4.2 24.6 1.0
CG A:MET165 4.2 27.4 1.0
C A:HIS164 4.2 20.5 1.0
CB A:HIS164 4.4 16.6 1.0
O A:ASP187 4.4 28.1 1.0
N A:ARG188 4.4 28.8 1.0
C20 A:RGQ407 4.5 31.8 0.9
CB A:HIS41 4.6 21.7 1.0
CA A:MET165 4.7 22.6 1.0
O A:HOH516 4.7 18.8 1.0
N A:MET165 4.8 21.0 1.0
CE1 A:HIS41 4.8 27.1 1.0
N A:ASP187 4.8 27.2 1.0
CA A:HIS164 4.9 17.7 1.0
O A:VAL186 4.9 27.7 1.0
ND1 A:HIS41 4.9 26.7 1.0

Chlorine binding site 3 out of 3 in 7gm4

Go back to Chlorine Binding Sites List in 7gm4
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 Alp-Pos-6F6AE286-5 (Mpro-P2080)


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 Alp-Pos-6F6AE286-5 (Mpro-P2080) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:40.4
occ:0.94
 CL B:RGQ405 0.0 40.4 0.9
C17 B:RGQ405 1.7 40.8 0.9
C18 B:RGQ405 2.7 40.9 0.9
C16 B:RGQ405 2.7 40.9 0.9
CD2 B:HIS41 3.4 32.0 1.0
CA B:ASP187 3.5 27.9 1.0
CB B:ASP187 3.6 29.5 1.0
O B:HIS164 3.7 20.5 1.0
CB B:MET165 3.8 23.6 1.0
C B:ASP187 3.8 31.6 1.0
SD B:MET165 3.9 42.0 1.0
C19 B:RGQ405 4.0 41.2 0.9
NE2 B:HIS41 4.0 33.2 1.0
C15 B:RGQ405 4.0 41.2 0.9
N B:ARG188 4.1 33.9 1.0
CG B:HIS41 4.2 30.8 1.0
CG B:MET165 4.2 28.3 1.0
C B:HIS164 4.2 19.7 1.0
CB B:HIS164 4.3 18.1 1.0
O B:ASP187 4.3 32.2 1.0
C20 B:RGQ405 4.5 41.4 0.9
CB B:HIS41 4.6 27.9 1.0
O B:HOH545 4.7 16.5 1.0
N B:MET165 4.8 20.1 1.0
CA B:MET165 4.8 21.7 1.0
O B:VAL186 4.8 23.6 1.0
N B:ASP187 4.8 24.9 1.0
CA B:HIS164 4.8 18.0 1.0
CE1 B:HIS41 4.8 33.3 1.0
CD2 B:HIS164 4.9 19.4 1.0
ND1 B:HIS41 5.0 32.9 1.0
CG B:ASP187 5.0 32.8 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 01:54:02 2025

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