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Chlorine in PDB 7gnm: 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 Nir-Wei-DCC3321B-2 (Mpro-P2761)

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 Nir-Wei-DCC3321B-2 (Mpro-P2761)

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 Nir-Wei-DCC3321B-2 (Mpro-P2761):
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 Nir-Wei-DCC3321B-2 (Mpro-P2761), PDB code: 7gnm 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) 72.03 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.836, 99.763, 104.119, 90, 90, 90
R / Rfree (%) 22.6 / 25.4

Other elements in 7gnm:

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 Nir-Wei-DCC3321B-2 (Mpro-P2761) also contains other interesting chemical elements:

Sodium (Na) 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 Nir-Wei-DCC3321B-2 (Mpro-P2761) (pdb code 7gnm). 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 Nir-Wei-DCC3321B-2 (Mpro-P2761), PDB code: 7gnm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gnm

Go back to Chlorine Binding Sites List in 7gnm
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 Nir-Wei-DCC3321B-2 (Mpro-P2761)


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 Nir-Wei-DCC3321B-2 (Mpro-P2761) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:26.6
occ:1.00
 NE2 A:GLN110 3.1 28.7 1.0
N A:GLN107 3.3 26.1 1.0
CA A:ILE106 3.6 25.7 1.0
CG A:GLN110 3.7 27.0 1.0
CB A:GLN110 3.8 25.8 1.0
CB A:ILE106 3.8 25.6 1.0
CD A:GLN110 3.9 28.7 1.0
C A:ILE106 3.9 26.1 1.0
CB A:GLN107 4.1 28.1 1.0
CG2 A:ILE106 4.1 25.1 1.0
CA A:GLN107 4.3 26.1 1.0
CG A:GLN107 4.3 30.4 1.0
O A:GLN107 4.6 26.2 1.0
O A:HOH604 4.6 52.1 1.0
O A:ARG105 4.7 28.0 1.0
O A:HOH747 4.8 35.6 1.0
C A:GLN107 4.9 26.9 1.0
N A:ILE106 4.9 25.5 1.0

Chlorine binding site 2 out of 3 in 7gnm

Go back to Chlorine Binding Sites List in 7gnm
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 Nir-Wei-DCC3321B-2 (Mpro-P2761)


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 Nir-Wei-DCC3321B-2 (Mpro-P2761) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:35.1
occ:0.82
 CL A:S1L408 0.0 35.1 0.8
C20 A:S1L408 1.7 35.3 0.8
C19 A:S1L408 2.7 35.1 0.8
C17 A:S1L408 2.7 36.0 0.8
CB A:ASP187 3.5 30.7 1.0
CA A:ASP187 3.5 31.6 1.0
ND1 A:HIS41 3.6 34.4 1.0
SD A:MET165 3.6 38.6 0.5
CB A:MET165 3.7 31.0 0.5
CB A:MET165 3.8 30.5 0.5
O A:HIS164 3.8 28.4 1.0
CE A:MET165 3.9 36.4 0.5
CE1 A:HIS41 3.9 35.4 1.0
SD A:MET165 3.9 40.8 0.5
C A:ASP187 4.0 33.8 1.0
C16 A:S1L408 4.0 36.4 0.8
CG A:MET165 4.0 34.1 0.5
C18 A:S1L408 4.0 35.4 0.8
CE A:MET49 4.0 58.8 1.0
CG A:MET165 4.2 33.2 0.5
C A:HIS164 4.3 28.3 1.0
N A:ARG188 4.3 35.1 1.0
CB A:HIS164 4.3 25.7 1.0
CG A:HIS41 4.3 32.3 1.0
C15 A:S1L408 4.5 36.7 0.8
O A:ASP187 4.5 34.0 1.0
O A:HOH539 4.6 27.1 1.0
N A:MET165 4.7 29.0 0.5
N A:MET165 4.7 28.9 0.5
CA A:MET165 4.7 29.5 0.5
CA A:MET165 4.7 29.7 0.5
NE2 A:HIS41 4.8 35.5 1.0
CB A:HIS41 4.8 29.3 1.0
N A:ASP187 4.8 31.1 1.0
CZ A:PHE181 4.8 27.0 1.0
O A:VAL186 4.8 31.2 1.0
CA A:HIS164 4.9 26.1 1.0
CD2 A:HIS164 4.9 23.4 1.0
CG A:ASP187 4.9 30.1 1.0
CD2 A:HIS41 5.0 33.5 1.0

Chlorine binding site 3 out of 3 in 7gnm

Go back to Chlorine Binding Sites List in 7gnm
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 Nir-Wei-DCC3321B-2 (Mpro-P2761)


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 Nir-Wei-DCC3321B-2 (Mpro-P2761) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:47.8
occ:0.82
 CL B:S1L407 0.0 47.8 0.8
C20 B:S1L407 1.7 47.8 0.8
C17 B:S1L407 2.7 47.9 0.8
C19 B:S1L407 2.7 47.6 0.8
CA B:ASP187 3.3 35.4 1.0
CB B:ASP187 3.4 34.5 1.0
ND1 B:HIS41 3.7 43.8 1.0
CB B:MET165 3.8 32.2 1.0
C B:ASP187 3.8 39.2 1.0
SD B:MET165 3.9 51.2 1.0
O B:HIS164 3.9 29.7 1.0
C16 B:S1L407 4.0 48.0 0.8
CG B:MET165 4.0 37.2 1.0
C18 B:S1L407 4.0 47.5 0.8
CE1 B:HIS41 4.0 44.1 1.0
N B:ARG188 4.2 41.5 1.0
CB B:HIS164 4.3 26.2 1.0
C B:HIS164 4.3 29.0 1.0
CE B:MET49 4.4 95.3 1.0
O B:VAL186 4.5 33.0 1.0
O B:ASP187 4.5 40.0 1.0
C15 B:S1L407 4.5 48.2 0.8
CG B:HIS41 4.5 41.5 1.0
N B:ASP187 4.6 33.3 1.0
N B:MET165 4.7 29.3 1.0
CA B:MET165 4.8 30.2 1.0
O B:HOH549 4.8 27.0 1.0
CD2 B:HIS164 4.9 26.5 1.0
CA B:HIS164 4.9 27.1 1.0
CG B:ASP187 4.9 35.4 1.0
CZ B:PHE181 4.9 27.1 1.0
NE2 B:HIS41 4.9 44.0 1.0
C B:VAL186 4.9 32.5 1.0
CB B:HIS41 5.0 39.1 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: Mon Jul 29 22:08:43 2024

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