Chlorine in PDB 7gkk: 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 Jin-Pos-6DC588A4-6 (Mpro-P0906)

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 Jin-Pos-6DC588A4-6 (Mpro-P0906)

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 Jin-Pos-6DC588A4-6 (Mpro-P0906):
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 Jin-Pos-6DC588A4-6 (Mpro-P0906), PDB code: 7gkk 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) 55.65 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.27, 99.04, 103.36, 90, 90, 90
R / Rfree (%) 23.9 / 27.7

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 Jin-Pos-6DC588A4-6 (Mpro-P0906) (pdb code 7gkk). 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 Jin-Pos-6DC588A4-6 (Mpro-P0906), PDB code: 7gkk:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gkk

Go back to Chlorine Binding Sites List in 7gkk
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 Jin-Pos-6DC588A4-6 (Mpro-P0906)


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 Jin-Pos-6DC588A4-6 (Mpro-P0906) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:31.6
occ:1.00
 NE2 A:GLN110 3.2 33.9 1.0
N A:GLN107 3.2 31.4 1.0
CA A:ILE106 3.7 31.3 1.0
CG A:GLN110 3.7 31.2 1.0
CB A:GLN110 3.8 28.8 1.0
CB A:ILE106 3.8 31.2 1.0
C A:ILE106 3.9 31.7 1.0
CD A:GLN110 3.9 34.0 1.0
CB A:GLN107 4.0 34.1 1.0
CA A:GLN107 4.2 31.9 1.0
CG2 A:ILE106 4.2 31.6 1.0
CG A:GLN107 4.2 38.4 1.0
O A:GLN107 4.5 30.7 1.0
O A:HOH679 4.6 41.2 1.0
O A:HOH564 4.7 56.2 1.0
O A:ARG105 4.8 33.5 1.0
C A:GLN107 4.9 31.4 1.0
N A:ILE106 4.9 31.3 1.0

Chlorine binding site 2 out of 3 in 7gkk

Go back to Chlorine Binding Sites List in 7gkk
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 Jin-Pos-6DC588A4-6 (Mpro-P0906)


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 Jin-Pos-6DC588A4-6 (Mpro-P0906) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:51.2
occ:1.00
 CL A:QXR408 0.0 51.2 1.0
C15 A:QXR408 1.7 50.5 1.0
C16 A:QXR408 2.7 49.8 1.0
C14 A:QXR408 2.7 50.6 1.0
CD2 A:HIS41 3.5 38.4 1.0
CA A:ASP187 3.5 38.1 1.0
CB A:ASP187 3.5 37.7 1.0
SD A:MET165 3.7 46.5 1.0
CB A:MET165 3.7 34.6 1.0
O A:HIS164 3.9 31.4 1.0
C A:ASP187 3.9 39.9 1.0
C13 A:QXR408 4.0 50.5 1.0
C11 A:QXR408 4.0 49.1 1.0
CE A:MET49 4.0 59.5 1.0
NE2 A:HIS41 4.0 39.6 1.0
CG A:HIS41 4.1 37.3 1.0
CG A:MET165 4.2 38.3 1.0
N A:ARG188 4.3 40.6 1.0
C A:HIS164 4.4 30.9 1.0
CB A:HIS41 4.5 35.1 1.0
O A:ASP187 4.5 39.8 1.0
C12 A:QXR408 4.5 50.0 1.0
CB A:HIS164 4.6 28.4 1.0
O A:HOH542 4.7 29.3 1.0
CA A:MET165 4.8 33.3 1.0
N A:ASP187 4.8 38.0 1.0
CE1 A:HIS41 4.8 39.4 1.0
N A:MET165 4.8 31.7 1.0
ND1 A:HIS41 4.9 38.9 1.0
O A:VAL186 4.9 38.0 1.0
CG A:ASP187 4.9 38.4 1.0

Chlorine binding site 3 out of 3 in 7gkk

Go back to Chlorine Binding Sites List in 7gkk
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 Jin-Pos-6DC588A4-6 (Mpro-P0906)


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 Jin-Pos-6DC588A4-6 (Mpro-P0906) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:60.1
occ:1.00
 CL B:QXR403 0.0 60.1 1.0
C15 B:QXR403 1.7 60.1 1.0
C14 B:QXR403 2.7 60.2 1.0
C16 B:QXR403 2.7 60.0 1.0
CA B:ASP187 3.4 40.9 1.0
CB B:ASP187 3.5 40.0 1.0
CD2 B:HIS41 3.5 46.9 1.0
C B:ASP187 3.7 44.4 1.0
CB B:MET165 3.9 36.3 1.0
SD B:MET165 3.9 54.1 1.0
N B:ARG188 4.0 46.7 1.0
O B:HIS164 4.0 35.1 1.0
C13 B:QXR403 4.0 60.3 1.0
C11 B:QXR403 4.0 59.9 1.0
CG B:HIS41 4.1 45.7 1.0
NE2 B:HIS41 4.1 48.1 1.0
O B:ASP187 4.2 45.1 1.0
CG B:MET165 4.3 41.2 1.0
CB B:HIS41 4.4 43.1 1.0
C B:HIS164 4.5 33.9 1.0
C12 B:QXR403 4.5 60.2 1.0
O B:HOH539 4.6 33.2 1.0
CB B:HIS164 4.7 31.4 1.0
N B:ASP187 4.7 39.1 1.0
O B:VAL186 4.8 38.2 1.0
CG B:ASP187 4.9 40.7 1.0
CE1 B:HIS41 4.9 48.3 1.0
CA B:MET165 4.9 35.0 1.0
ND1 B:HIS41 4.9 47.8 1.0
CA B:ARG188 4.9 49.9 1.0
N B:MET165 5.0 33.8 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: Mon Jul 29 21:47:07 2024

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