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Chlorine in PDB 7gkn: 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 Edj-Med-611D11E7-4 (Mpro-P0978)

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 Edj-Med-611D11E7-4 (Mpro-P0978)

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 Edj-Med-611D11E7-4 (Mpro-P0978):
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 Edj-Med-611D11E7-4 (Mpro-P0978), PDB code: 7gkn 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) 71.51 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.3, 99, 103.4, 90, 90, 90
R / Rfree (%) 23.8 / 27.4

Other elements in 7gkn:

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 Edj-Med-611D11E7-4 (Mpro-P0978) 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 Edj-Med-611D11E7-4 (Mpro-P0978) (pdb code 7gkn). 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 Edj-Med-611D11E7-4 (Mpro-P0978), PDB code: 7gkn:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gkn

Go back to Chlorine Binding Sites List in 7gkn
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 Edj-Med-611D11E7-4 (Mpro-P0978)


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 Edj-Med-611D11E7-4 (Mpro-P0978) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:30.5
occ:1.00
 N A:GLN107 3.1 31.6 1.0
NE2 A:GLN110 3.1 31.7 1.0
CA A:ILE106 3.6 30.0 1.0
CG A:GLN110 3.8 29.8 1.0
CB A:GLN110 3.8 28.9 1.0
CB A:ILE106 3.8 29.5 1.0
C A:ILE106 3.8 30.8 1.0
CD A:GLN110 3.9 32.3 1.0
CB A:GLN107 4.0 35.0 1.0
CG2 A:ILE106 4.1 29.9 1.0
CA A:GLN107 4.1 32.4 1.0
CG A:GLN107 4.1 40.2 1.0
O A:GLN107 4.4 33.5 1.0
O A:HOH548 4.6 53.0 1.0
O A:HOH672 4.7 37.3 1.0
O A:ARG105 4.7 32.8 1.0
C A:GLN107 4.8 32.9 1.0
N A:ILE106 4.9 30.0 1.0

Chlorine binding site 2 out of 3 in 7gkn

Go back to Chlorine Binding Sites List in 7gkn
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 Edj-Med-611D11E7-4 (Mpro-P0978)


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 Edj-Med-611D11E7-4 (Mpro-P0978) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:43.3
occ:1.00
 CL A:QYI407 0.0 43.3 1.0
C7 A:QYI407 1.7 44.3 1.0
C8 A:QYI407 2.7 45.0 1.0
C6 A:QYI407 2.7 45.0 1.0
CB A:ASP187 3.4 36.0 1.0
CD2 A:HIS41 3.5 37.0 1.0
CA A:ASP187 3.5 36.7 1.0
O A:HIS164 3.5 32.4 1.0
CB A:MET165 3.6 34.8 1.0
SD A:MET165 3.9 45.4 1.0
C A:HIS164 3.9 31.5 1.0
CB A:HIS164 4.0 28.6 1.0
C5 A:QYI407 4.0 45.6 1.0
C9 A:QYI407 4.0 45.7 1.0
NE2 A:HIS41 4.0 38.5 1.0
CG A:MET165 4.1 39.4 1.0
C A:ASP187 4.2 38.7 1.0
CZ A:PHE181 4.3 32.5 1.0
CA A:MET165 4.4 33.0 1.0
CG A:HIS41 4.4 35.8 1.0
N A:MET165 4.4 31.5 1.0
C4 A:QYI407 4.5 46.0 1.0
CE A:MET49 4.5 56.0 1.0
CA A:HIS164 4.6 29.2 1.0
O A:VAL186 4.6 36.9 1.0
N A:ASP187 4.6 36.6 1.0
N A:ARG188 4.6 39.7 1.0
O A:HOH564 4.6 26.8 1.0
O A:ASP187 4.8 39.0 1.0
CG A:HIS164 4.8 28.7 1.0
CD2 A:HIS164 4.8 28.4 1.0
CG A:ASP187 4.9 36.0 1.0
C A:QYI407 4.9 46.7 1.0
CB A:HIS41 4.9 34.1 1.0
CE A:MET165 5.0 36.7 1.0

Chlorine binding site 3 out of 3 in 7gkn

Go back to Chlorine Binding Sites List in 7gkn
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 Edj-Med-611D11E7-4 (Mpro-P0978)


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 Edj-Med-611D11E7-4 (Mpro-P0978) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:49.9
occ:1.00
 CL B:QYI404 0.0 49.9 1.0
C7 B:QYI404 1.7 51.1 1.0
C6 B:QYI404 2.7 51.6 1.0
C8 B:QYI404 2.7 52.1 1.0
CB B:ASP187 3.4 39.7 1.0
CA B:ASP187 3.4 39.7 1.0
CB B:MET165 3.6 36.8 1.0
CD2 B:HIS41 3.6 44.6 1.0
O B:HIS164 3.7 34.2 1.0
C5 B:QYI404 4.0 52.3 1.0
C9 B:QYI404 4.0 52.9 1.0
CB B:HIS164 4.0 31.2 1.0
C B:HIS164 4.0 33.2 1.0
C B:ASP187 4.1 43.0 1.0
CG B:MET165 4.1 42.7 1.0
NE2 B:HIS41 4.1 46.2 1.0
SD B:MET165 4.1 56.1 1.0
CE B:MET49 4.4 76.9 1.0
N B:ARG188 4.4 45.4 1.0
C4 B:QYI404 4.5 52.9 1.0
CG B:HIS41 4.5 43.6 1.0
N B:MET165 4.5 33.4 1.0
O B:VAL186 4.5 35.9 1.0
CZ B:PHE181 4.5 33.1 1.0
CA B:MET165 4.6 34.7 1.0
N B:ASP187 4.6 37.6 1.0
CA B:HIS164 4.6 31.6 1.0
O B:ASP187 4.7 43.1 1.0
O B:HOH532 4.7 28.9 1.0
CG B:ASP187 4.8 41.9 1.0
CG B:HIS164 4.9 32.1 1.0
CD2 B:HIS164 4.9 33.2 1.0
C B:VAL186 5.0 36.6 1.0
CB B:HIS41 5.0 41.0 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 01:44:48 2025

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