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Chlorine in PDB 7gmd: 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-7174C657-6 (Mpro-P2176)

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-7174C657-6 (Mpro-P2176)

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-7174C657-6 (Mpro-P2176):
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-7174C657-6 (Mpro-P2176), PDB code: 7gmd 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) 37.59 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.878, 100.2, 104.168, 90, 90, 90
R / Rfree (%) 21.5 / 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-7174C657-6 (Mpro-P2176) (pdb code 7gmd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 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-7174C657-6 (Mpro-P2176), PDB code: 7gmd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7gmd

Go back to Chlorine Binding Sites List in 7gmd
Chlorine binding site 1 out of 2 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-7174C657-6 (Mpro-P2176)


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-7174C657-6 (Mpro-P2176) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:26.2
occ:1.00
 N A:GLN107 3.2 24.8 1.0
NE2 A:GLN110 3.3 27.2 1.0
CA A:ILE106 3.7 24.7 1.0
CB A:GLN110 3.8 22.9 1.0
CG A:GLN110 3.8 24.7 1.0
C A:ILE106 3.9 24.9 1.0
CB A:ILE106 4.0 24.4 1.0
CB A:GLN107 4.0 26.8 1.0
CD A:GLN110 4.1 27.3 1.0
CA A:GLN107 4.2 25.6 1.0
CG A:GLN107 4.2 32.3 1.0
CG2 A:ILE106 4.3 23.7 1.0
O A:GLN107 4.5 26.5 1.0
O A:ARG105 4.8 27.3 1.0
C A:GLN107 4.8 26.1 1.0
O A:HOH647 4.8 30.1 1.0

Chlorine binding site 2 out of 2 in 7gmd

Go back to Chlorine Binding Sites List in 7gmd
Chlorine binding site 2 out of 2 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-7174C657-6 (Mpro-P2176)


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-7174C657-6 (Mpro-P2176) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:46.5
occ:0.80
 CL A:R2X408 0.0 46.5 0.8
C A:R2X408 1.7 45.4 0.8
C5 A:R2X408 2.7 44.4 0.8
C1 A:R2X408 2.7 45.1 0.8
CD2 A:HIS41 3.3 34.2 1.0
CB A:ASP187 3.5 30.9 1.0
CA A:ASP187 3.6 31.8 1.0
CG A:HIS41 3.7 32.8 1.0
C A:ASP187 3.9 32.5 1.0
NE2 A:HIS41 3.9 35.1 1.0
C2 A:R2X408 4.0 44.7 0.8
C4 A:R2X408 4.0 43.6 0.8
CB A:HIS41 4.0 30.1 1.0
SD A:MET165 4.1 41.9 1.0
O A:HIS164 4.1 27.7 1.0
CB A:MET165 4.2 30.4 1.0
O A:ASP187 4.3 32.4 1.0
N A:ARG188 4.4 33.5 1.0
ND1 A:HIS41 4.4 34.5 1.0
C3 A:R2X408 4.5 44.2 0.8
CE1 A:HIS41 4.5 34.9 1.0
O A:HOH535 4.5 21.8 1.0
CG A:MET165 4.7 34.4 1.0
C A:HIS164 4.7 26.7 1.0
CG A:ASP187 4.9 31.6 1.0
CB A:HIS164 4.9 24.1 1.0
N A:ASP187 4.9 32.4 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 01:55:23 2025

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