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Chlorine in PDB 7gnp: 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-5 (Mpro-P2889)

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-5 (Mpro-P2889)

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-5 (Mpro-P2889):
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-5 (Mpro-P2889), PDB code: 7gnp 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) 72.72 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.951, 100.938, 104.843, 90, 90, 90
R / Rfree (%) 23.2 / 26

Other elements in 7gnp:

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-5 (Mpro-P2889) 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-5 (Mpro-P2889) (pdb code 7gnp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 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-5 (Mpro-P2889), PDB code: 7gnp:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7gnp

Go back to Chlorine Binding Sites List in 7gnp
Chlorine binding site 1 out of 4 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-5 (Mpro-P2889)


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-5 (Mpro-P2889) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:28.4
occ:1.00
 O A:HOH798 3.1 56.3 1.0
N A:GLN107 3.3 25.4 1.0
NE2 A:GLN110 3.3 29.1 1.0
CA A:ILE106 3.8 24.7 1.0
CB A:GLN110 3.8 22.9 1.0
CG A:GLN110 3.9 25.4 1.0
CB A:ILE106 4.0 24.5 1.0
CB A:GLN107 4.0 28.5 1.0
C A:ILE106 4.0 25.9 1.0
CG A:GLN107 4.1 32.5 1.0
CD A:GLN110 4.1 28.8 1.0
CA A:GLN107 4.2 26.8 1.0
CG2 A:ILE106 4.3 24.2 1.0
O A:GLN107 4.6 28.6 1.0
O A:HOH772 4.8 33.8 1.0
O A:ARG105 4.9 26.0 1.0
C A:GLN107 4.9 28.6 1.0

Chlorine binding site 2 out of 4 in 7gnp

Go back to Chlorine Binding Sites List in 7gnp
Chlorine binding site 2 out of 4 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-5 (Mpro-P2889)


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-5 (Mpro-P2889) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:31.8
occ:0.99
 CL A:S4X406 0.0 31.8 1.0
C30 A:S4X406 1.7 30.6 1.0
C29 A:S4X406 2.7 30.3 1.0
C27 A:S4X406 2.7 30.9 1.0
CB A:ASP187 3.4 28.8 1.0
CA A:ASP187 3.4 28.8 1.0
ND1 A:HIS41 3.6 31.7 1.0
O A:HIS164 3.8 25.7 1.0
SD A:MET165 3.9 36.7 1.0
C A:ASP187 3.9 31.2 1.0
CB A:MET165 4.0 24.4 1.0
C26 A:S4X406 4.0 31.2 1.0
C28 A:S4X406 4.0 30.2 1.0
CE1 A:HIS41 4.0 32.3 1.0
CE A:MET49 4.0 41.6 1.0
CE A:MET165 4.3 34.3 1.0
CG A:HIS41 4.3 28.7 1.0
CB A:HIS164 4.3 22.9 1.0
N A:ARG188 4.4 32.3 1.0
C A:HIS164 4.4 23.6 1.0
O A:ASP187 4.5 31.2 1.0
O A:HOH574 4.5 25.9 1.0
C25 A:S4X406 4.5 30.9 1.0
CG A:MET165 4.5 26.3 1.0
N A:ASP187 4.7 28.9 1.0
CB A:HIS41 4.7 26.6 1.0
O A:VAL186 4.7 29.9 1.0
CG A:ASP187 4.9 28.4 1.0
NE2 A:HIS41 4.9 31.9 1.0
CD2 A:HIS164 4.9 22.6 1.0
CZ A:PHE181 4.9 26.1 1.0
CA A:MET165 5.0 24.5 1.0
N A:MET165 5.0 23.2 1.0

Chlorine binding site 3 out of 4 in 7gnp

Go back to Chlorine Binding Sites List in 7gnp
Chlorine binding site 3 out of 4 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-5 (Mpro-P2889)


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-5 (Mpro-P2889) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:65.0
occ:1.00
 C A:THR190 3.7 42.7 1.0
CA A:THR190 3.8 40.8 1.0
NE2 A:GLN189 3.8 41.5 1.0
N A:ALA191 3.9 42.0 1.0
N A:THR190 4.0 38.2 1.0
O A:GLN189 4.1 36.9 1.0
O A:THR190 4.1 44.0 1.0
C A:GLN189 4.2 36.5 1.0
CG A:GLN189 4.3 38.5 1.0
CD A:GLN189 4.6 41.6 1.0
CA A:ALA191 4.6 42.1 1.0

Chlorine binding site 4 out of 4 in 7gnp

Go back to Chlorine Binding Sites List in 7gnp
Chlorine binding site 4 out of 4 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-5 (Mpro-P2889)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 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-5 (Mpro-P2889) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:28.3
occ:0.87
 CL B:S4X405 0.0 28.3 0.9
C30 B:S4X405 1.7 27.2 0.9
C29 B:S4X405 2.7 26.9 0.9
C27 B:S4X405 2.7 27.6 0.9
CB B:ASP187 3.4 26.4 1.0
CA B:ASP187 3.5 27.2 1.0
ND1 B:HIS41 3.7 30.2 1.0
CB B:MET165 3.7 24.1 0.5
CB B:MET165 3.8 22.6 0.5
SD B:MET165 3.9 36.8 0.5
O B:HIS164 4.0 24.3 1.0
CG B:MET165 4.0 28.1 0.5
C26 B:S4X405 4.0 27.9 0.9
C28 B:S4X405 4.0 26.8 0.9
C B:ASP187 4.1 30.1 1.0
CE1 B:HIS41 4.1 30.7 1.0
CB B:HIS164 4.1 20.9 1.0
CE B:MET49 4.2 48.0 1.0
C B:HIS164 4.3 21.7 1.0
N B:ARG188 4.4 31.9 1.0
SD B:MET165 4.4 27.2 0.5
CG B:MET165 4.4 24.5 0.5
C25 B:S4X405 4.5 27.7 0.9
CG B:HIS41 4.5 28.8 1.0
O B:VAL186 4.5 26.2 1.0
CZ B:PHE181 4.6 23.9 1.0
N B:ASP187 4.6 26.0 1.0
CD2 B:HIS164 4.7 22.8 1.0
O B:ASP187 4.7 30.1 1.0
N B:MET165 4.7 21.9 0.5
O B:HOH549 4.7 22.9 1.0
N B:MET165 4.7 21.6 0.5
CA B:MET165 4.8 22.4 0.5
CA B:MET165 4.8 23.0 0.5
CA B:HIS164 4.8 20.6 1.0
CG B:HIS164 4.8 22.9 1.0
CG B:ASP187 4.9 28.7 1.0
CB B:HIS41 5.0 27.7 1.0
C B:VAL186 5.0 25.9 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 22:08:52 2024

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