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Chlorine in PDB 7gm9: 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-1BED62CF-3 (Mpro-P2113)

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-1BED62CF-3 (Mpro-P2113)

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-1BED62CF-3 (Mpro-P2113):
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-1BED62CF-3 (Mpro-P2113), PDB code: 7gm9 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) 72.58 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.93, 101.14, 104.224, 90, 90, 90
R / Rfree (%) 22.4 / 25.1

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-1BED62CF-3 (Mpro-P2113) (pdb code 7gm9). 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-1BED62CF-3 (Mpro-P2113), PDB code: 7gm9:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gm9

Go back to Chlorine Binding Sites List in 7gm9
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-1BED62CF-3 (Mpro-P2113)


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-1BED62CF-3 (Mpro-P2113) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:27.9
occ:1.00
 NE2 A:GLN110 3.2 30.6 1.0
N A:GLN107 3.3 23.0 1.0
CG A:GLN110 3.7 25.6 1.0
CB A:GLN110 3.7 21.5 1.0
CA A:ILE106 3.8 22.8 1.0
CB A:ILE106 3.9 22.4 1.0
CD A:GLN110 4.0 30.5 1.0
C A:ILE106 4.0 23.2 1.0
CB A:GLN107 4.1 24.9 1.0
CG2 A:ILE106 4.2 22.4 1.0
CG A:GLN107 4.2 28.7 1.0
CA A:GLN107 4.3 23.5 1.0
O A:GLN107 4.6 23.7 1.0
O A:ARG105 4.8 25.4 1.0
C A:GLN107 4.9 24.2 1.0

Chlorine binding site 2 out of 3 in 7gm9

Go back to Chlorine Binding Sites List in 7gm9
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-1BED62CF-3 (Mpro-P2113)


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-1BED62CF-3 (Mpro-P2113) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:41.2
occ:0.90
 CL A:RIJ407 0.0 41.2 0.9
C7 A:RIJ407 1.7 42.0 0.9
C6 A:RIJ407 2.7 42.6 0.9
C8 A:RIJ407 2.7 42.1 0.9
CD2 A:HIS41 3.4 33.4 1.0
CB A:ASP187 3.5 30.8 1.0
O A:HIS164 3.5 27.1 1.0
CA A:ASP187 3.6 30.9 1.0
NE2 A:HIS41 3.8 35.2 1.0
CB A:MET165 3.9 29.3 1.0
CG A:HIS41 3.9 31.2 1.0
SD A:MET165 3.9 40.0 1.0
C5 A:RIJ407 4.0 43.0 0.9
C9 A:RIJ407 4.0 42.2 0.9
C A:HIS164 4.1 25.9 1.0
CE A:MET49 4.1 51.5 1.0
C A:ASP187 4.1 32.9 1.0
CB A:HIS164 4.2 22.0 1.0
CG A:MET165 4.2 32.2 1.0
O A:HOH526 4.3 25.1 1.0
CB A:HIS41 4.5 26.4 1.0
C4 A:RIJ407 4.5 43.0 0.9
CE1 A:HIS41 4.5 35.4 1.0
O A:ASP187 4.6 32.9 1.0
ND1 A:HIS41 4.6 34.2 1.0
CA A:HIS164 4.6 22.8 1.0
N A:MET165 4.7 26.4 1.0
N A:ARG188 4.7 34.0 1.0
CD2 A:HIS164 4.8 20.7 1.0
CA A:MET165 4.8 27.8 1.0
CG A:ASP187 4.9 32.6 1.0
CG A:HIS164 4.9 20.9 1.0
N A:ASP187 4.9 30.7 1.0

Chlorine binding site 3 out of 3 in 7gm9

Go back to Chlorine Binding Sites List in 7gm9
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-1BED62CF-3 (Mpro-P2113)


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-1BED62CF-3 (Mpro-P2113) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:39.8
occ:0.80
 CL B:RIJ403 0.0 39.8 0.8
C7 B:RIJ403 1.7 39.6 0.8
C6 B:RIJ403 2.7 39.8 0.8
C8 B:RIJ403 2.7 39.6 0.8
ND1 B:HIS41 3.1 40.7 0.5
CE1 B:HIS41 3.5 41.5 0.5
O B:HIS164 3.6 28.9 1.0
CB B:ASP187 3.7 35.6 1.0
CG B:HIS41 3.7 38.9 0.5
CA B:ASP187 3.9 34.9 1.0
CB B:HIS164 4.0 24.1 1.0
C B:HIS164 4.0 27.7 1.0
C5 B:RIJ403 4.0 40.0 0.8
C9 B:RIJ403 4.0 39.7 0.8
CB B:MET165 4.0 30.6 1.0
CB B:HIS41 4.1 36.7 0.5
CG B:HIS41 4.1 38.9 0.5
O B:HOH536 4.2 20.3 1.0
CB B:HIS41 4.2 36.6 0.5
ND1 B:HIS41 4.2 40.6 0.5
NE2 B:HIS41 4.3 41.5 0.5
C B:ASP187 4.3 39.3 1.0
SD B:MET165 4.3 46.6 1.0
CD2 B:HIS41 4.4 40.3 0.5
CA B:HIS164 4.4 24.9 1.0
CD2 B:HIS164 4.4 24.7 1.0
CG B:MET165 4.5 34.8 1.0
C4 B:RIJ403 4.5 40.3 0.8
CG B:HIS164 4.6 24.4 1.0
N B:MET165 4.6 28.0 1.0
N B:ARG188 4.7 41.5 1.0
CD2 B:HIS41 4.8 40.0 0.5
O B:ASP187 4.8 40.8 1.0
CA B:MET165 4.8 28.9 1.0
CE1 B:HIS41 4.8 41.0 0.5

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 01:54:42 2025

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