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Chlorine in PDB 7gkf: 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-Uni-8D415491-6 (Mpro-P0872)

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-Uni-8D415491-6 (Mpro-P0872)

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-Uni-8D415491-6 (Mpro-P0872):
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-Uni-8D415491-6 (Mpro-P0872), PDB code: 7gkf 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) 35.72 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.25, 98.77, 103.43, 90, 90, 90
R / Rfree (%) 23.1 / 26.3

Other elements in 7gkf:

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-Uni-8D415491-6 (Mpro-P0872) also contains other interesting chemical elements:

Fluorine (F) 1 atom

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-Uni-8D415491-6 (Mpro-P0872) (pdb code 7gkf). 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-Uni-8D415491-6 (Mpro-P0872), PDB code: 7gkf:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gkf

Go back to Chlorine Binding Sites List in 7gkf
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-Uni-8D415491-6 (Mpro-P0872)


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-Uni-8D415491-6 (Mpro-P0872) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:31.1
occ:1.00
 NE2 A:GLN110 3.2 27.6 1.0
N A:GLN107 3.2 29.8 1.0
CA A:ILE106 3.7 28.9 1.0
CB A:GLN110 3.7 27.7 1.0
CG A:GLN110 3.8 27.9 1.0
CB A:ILE106 3.9 28.8 1.0
C A:ILE106 3.9 29.9 1.0
CB A:GLN107 4.0 32.1 1.0
CD A:GLN110 4.0 28.6 1.0
CA A:GLN107 4.1 30.5 1.0
CG2 A:ILE106 4.2 28.7 1.0
CG A:GLN107 4.2 36.2 1.0
O A:GLN107 4.5 29.9 1.0
O A:HOH669 4.6 39.4 1.0
O A:HOH549 4.6 46.1 1.0
O A:ARG105 4.8 30.3 1.0
C A:GLN107 4.8 30.6 1.0
N A:ILE106 5.0 28.3 1.0

Chlorine binding site 2 out of 3 in 7gkf

Go back to Chlorine Binding Sites List in 7gkf
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-Uni-8D415491-6 (Mpro-P0872)


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-Uni-8D415491-6 (Mpro-P0872) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:44.7
occ:0.82
 CL1 A:QWL408 0.0 44.7 0.8
C14 A:QWL408 1.7 45.6 0.8
C15 A:QWL408 2.7 45.1 0.8
C13 A:QWL408 2.7 47.1 0.8
CL A:QWL408 3.2 48.8 0.8
CD2 A:HIS41 3.2 37.7 1.0
CB A:ASP187 3.6 35.6 1.0
CA A:ASP187 3.8 36.3 1.0
CB A:MET165 3.8 30.9 1.0
O A:HIS164 3.8 30.9 1.0
NE2 A:HIS41 3.8 39.2 1.0
SD A:MET165 3.9 44.9 1.0
CG A:HIS41 3.9 36.7 1.0
C16 A:QWL408 4.0 45.0 0.8
C12 A:QWL408 4.0 46.5 0.8
CE A:MET49 4.2 68.3 1.0
C A:ASP187 4.2 37.5 1.0
C A:HIS164 4.3 30.0 1.0
CB A:HIS41 4.3 34.6 1.0
CG A:MET165 4.4 34.8 1.0
C11 A:QWL408 4.5 45.8 0.8
CB A:HIS164 4.5 27.4 1.0
O A:HOH570 4.6 25.5 1.0
O A:ASP187 4.6 37.9 1.0
CE1 A:HIS41 4.6 39.3 1.0
ND1 A:HIS41 4.7 38.8 1.0
N A:ARG188 4.7 38.6 1.0
CA A:MET165 4.8 30.9 1.0
N A:MET165 4.8 30.1 1.0
CA A:HIS164 4.9 27.7 1.0

Chlorine binding site 3 out of 3 in 7gkf

Go back to Chlorine Binding Sites List in 7gkf
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-Uni-8D415491-6 (Mpro-P0872)


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-Uni-8D415491-6 (Mpro-P0872) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:48.8
occ:0.82
 CL A:QWL408 0.0 48.8 0.8
C13 A:QWL408 1.7 47.1 0.8
C12 A:QWL408 2.7 46.5 0.8
C14 A:QWL408 2.7 45.6 0.8
C A:ARG188 3.0 41.7 1.0
CE A:MET49 3.1 68.3 1.0
O A:ARG188 3.1 41.0 1.0
CL1 A:QWL408 3.2 44.7 0.8
N A:ARG188 3.3 38.6 1.0
N A:GLN189 3.4 44.0 1.0
CA A:ARG188 3.6 40.0 1.0
C A:ASP187 3.7 37.5 1.0
CA A:GLN189 3.9 47.5 1.0
C11 A:QWL408 4.0 45.8 0.8
C1 A:DMS403 4.0 73.1 1.0
C15 A:QWL408 4.0 45.1 0.8
CG A:GLN189 4.1 56.0 1.0
CA A:ASP187 4.2 36.3 1.0
SD A:MET165 4.3 44.9 1.0
O A:ASP187 4.3 37.9 1.0
C2 A:DMS403 4.4 73.0 1.0
CB A:GLN189 4.5 50.2 1.0
C16 A:QWL408 4.5 45.0 0.8
O A:VAL186 4.6 37.8 1.0
CD A:GLN189 4.8 61.8 1.0
SD A:MET49 4.8 70.3 1.0
NE2 A:GLN189 4.9 63.1 1.0
O A:MET49 4.9 57.4 1.0
NE2 A:GLN192 4.9 48.1 1.0
S A:DMS403 5.0 73.3 1.0
CB A:MET165 5.0 30.9 1.0
CB A:ASP187 5.0 35.6 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 01:43:29 2025

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