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Chlorine in PDB 7gkb: 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-96F51285-5 (Mpro-P0831)

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-96F51285-5 (Mpro-P0831)

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-96F51285-5 (Mpro-P0831):
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-96F51285-5 (Mpro-P0831), PDB code: 7gkb 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) 37.86 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.29, 98.74, 103.4, 90, 90, 90
R / Rfree (%) 23.9 / 28.5

Other elements in 7gkb:

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-96F51285-5 (Mpro-P0831) also contains other interesting chemical elements:

Fluorine (F) 4 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 Mat-Pos-96F51285-5 (Mpro-P0831) (pdb code 7gkb). 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-96F51285-5 (Mpro-P0831), PDB code: 7gkb:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gkb

Go back to Chlorine Binding Sites List in 7gkb
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-96F51285-5 (Mpro-P0831)


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-96F51285-5 (Mpro-P0831) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:32.8
occ:1.00
 NE2 A:GLN110 3.1 32.8 1.0
N A:GLN107 3.2 32.0 1.0
CA A:ILE106 3.7 31.4 1.0
CB A:GLN110 3.8 29.1 1.0
CG A:GLN110 3.9 30.6 1.0
CB A:ILE106 3.9 31.8 1.0
CB A:GLN107 3.9 33.6 1.0
C A:ILE106 3.9 32.3 1.0
CD A:GLN110 3.9 32.0 1.0
CG A:GLN107 4.0 38.3 1.0
CA A:GLN107 4.1 32.4 1.0
CG2 A:ILE106 4.3 31.7 1.0
O A:HOH584 4.4 50.9 1.0
O A:GLN107 4.5 33.2 1.0
O A:HOH653 4.6 39.1 1.0
O A:ARG105 4.8 33.2 1.0
C A:GLN107 4.8 32.8 1.0

Chlorine binding site 2 out of 3 in 7gkb

Go back to Chlorine Binding Sites List in 7gkb
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-96F51285-5 (Mpro-P0831)


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-96F51285-5 (Mpro-P0831) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:41.1
occ:0.75
 CL A:QVG408 0.0 41.1 0.8
C14 A:QVG408 1.7 41.6 0.8
C13 A:QVG408 2.7 42.0 0.8
C15 A:QVG408 2.7 41.5 0.8
F1 A:QVG408 2.9 42.3 0.8
CD2 A:HIS41 3.3 41.1 1.0
CB A:ASP187 3.5 41.0 1.0
CA A:ASP187 3.7 41.3 1.0
CB A:MET165 3.8 34.8 1.0
O A:HIS164 3.8 34.6 1.0
SD A:MET165 3.9 42.3 1.0
CG A:HIS41 3.9 40.2 1.0
NE2 A:HIS41 3.9 42.4 1.0
C12 A:QVG408 4.0 41.9 0.8
C16 A:QVG408 4.0 41.5 0.8
CE A:MET49 4.0 69.2 1.0
C A:ASP187 4.1 42.3 1.0
CG A:MET165 4.2 37.2 1.0
C A:HIS164 4.3 33.7 1.0
CB A:HIS41 4.3 37.8 1.0
CB A:HIS164 4.4 31.2 1.0
C11 A:QVG408 4.5 41.9 0.8
N A:ARG188 4.6 42.9 1.0
CE1 A:HIS41 4.6 42.6 1.0
ND1 A:HIS41 4.6 42.3 1.0
O A:HOH526 4.6 22.7 1.0
O A:ASP187 4.7 42.8 1.0
CA A:MET165 4.8 35.0 1.0
N A:MET165 4.8 34.3 1.0
CA A:HIS164 4.9 31.6 1.0
CG A:ASP187 4.9 42.6 1.0
N A:ASP187 5.0 40.9 1.0
CD2 A:HIS164 5.0 30.2 1.0

Chlorine binding site 3 out of 3 in 7gkb

Go back to Chlorine Binding Sites List in 7gkb
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-96F51285-5 (Mpro-P0831)


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-96F51285-5 (Mpro-P0831) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:61.1
occ:0.75
 CL B:QVG403 0.0 61.1 0.8
C14 B:QVG403 1.7 61.4 0.8
C13 B:QVG403 2.7 61.7 0.8
C15 B:QVG403 2.7 61.6 0.8
F1 B:QVG403 2.9 61.9 0.8
CD2 B:HIS41 3.3 46.7 1.0
CB B:ASP187 3.5 42.9 1.0
CA B:ASP187 3.6 43.2 1.0
O B:HIS164 3.7 35.4 1.0
CG B:HIS41 3.9 45.2 1.0
CB B:MET165 3.9 38.1 1.0
NE2 B:HIS41 3.9 48.2 1.0
C B:ASP187 3.9 46.7 1.0
C12 B:QVG403 4.0 61.8 0.8
C16 B:QVG403 4.0 61.8 0.8
SD B:MET165 4.0 52.4 1.0
C B:HIS164 4.3 35.7 1.0
CB B:HIS41 4.3 42.4 1.0
O B:ASP187 4.3 47.4 1.0
N B:ARG188 4.4 48.9 1.0
CB B:HIS164 4.4 34.6 1.0
CG B:MET165 4.4 42.0 1.0
C11 B:QVG403 4.5 61.9 0.8
O B:HOH521 4.5 33.3 1.0
CE1 B:HIS41 4.6 48.3 1.0
ND1 B:HIS41 4.6 47.6 1.0
O B:HOH556 4.8 56.7 1.0
CA B:MET165 4.8 36.8 1.0
N B:MET165 4.8 36.0 1.0
CG B:ASP187 4.9 43.5 1.0
CA B:HIS164 4.9 34.3 1.0
N B:ASP187 4.9 41.1 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 01:42:39 2025

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