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Chlorine in PDB 7gi3: 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 Mat-Pos-090737B9-1 (Mpro-P0041)

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 Mat-Pos-090737B9-1 (Mpro-P0041)

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 Mat-Pos-090737B9-1 (Mpro-P0041):
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 Mat-Pos-090737B9-1 (Mpro-P0041), PDB code: 7gi3 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) 71.36 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.29, 98.63, 103.39, 90, 90, 90
R / Rfree (%) 22.1 / 26.2

Other elements in 7gi3:

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 Mat-Pos-090737B9-1 (Mpro-P0041) also contains other interesting chemical elements:

Calcium (Ca) 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 Mat-Pos-090737B9-1 (Mpro-P0041) (pdb code 7gi3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 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 Mat-Pos-090737B9-1 (Mpro-P0041), PDB code: 7gi3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 7gi3

Go back to Chlorine Binding Sites List in 7gi3
Chlorine binding site 1 out of 7 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 Mat-Pos-090737B9-1 (Mpro-P0041)


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 Mat-Pos-090737B9-1 (Mpro-P0041) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:44.5
occ:0.70
 CL A:Q0I404 0.0 44.5 0.7
C10 A:Q0I404 1.7 44.6 0.7
C11 A:Q0I404 2.7 44.7 0.7
C9 A:Q0I404 2.7 44.4 0.7
CD2 A:HIS41 3.3 41.6 1.0
CB A:ASP187 3.4 43.8 1.0
O A:HIS164 3.6 38.5 1.0
CA A:ASP187 3.6 44.1 1.0
NE2 A:HIS41 3.8 42.9 1.0
CB A:MET165 3.8 40.9 1.0
C12 A:Q0I404 4.0 44.9 0.7
C8 A:Q0I404 4.0 44.4 0.7
CG A:HIS41 4.0 41.1 1.0
SD A:MET165 4.1 51.2 1.0
C A:HIS164 4.1 37.5 1.0
C A:ASP187 4.1 45.3 1.0
CB A:HIS164 4.2 33.8 1.0
CG A:MET165 4.2 44.0 1.0
CE A:MET49 4.4 70.6 1.0
O A:HOH522 4.5 31.1 1.0
C7 A:Q0I404 4.5 44.9 0.7
O A:ASP187 4.5 45.1 1.0
CB A:HIS41 4.5 38.9 1.0
CE1 A:HIS41 4.6 43.3 1.0
N A:ARG188 4.6 46.6 1.0
N A:MET165 4.6 38.5 1.0
CA A:HIS164 4.7 34.6 1.0
CA A:MET165 4.7 39.9 1.0
ND1 A:HIS41 4.8 43.5 1.0
CG A:ASP187 4.8 44.6 1.0
CD2 A:HIS164 4.8 34.2 1.0
N A:ASP187 4.9 44.1 1.0
CZ A:PHE181 4.9 36.4 1.0
CG A:HIS164 4.9 34.1 1.0
O A:VAL186 5.0 43.1 1.0

Chlorine binding site 2 out of 7 in 7gi3

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Chlorine binding site 2 out of 7 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 Mat-Pos-090737B9-1 (Mpro-P0041)


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 Mat-Pos-090737B9-1 (Mpro-P0041) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl415

b:70.2
occ:1.00
 O A:LEU287 3.2 35.8 1.0
O A:HOH538 3.2 61.2 1.0
N A:LEU287 3.9 36.6 1.0
C A:LEU287 4.1 36.1 1.0
C1 A:DMS407 4.3 79.2 1.0
CB A:LEU287 4.3 35.8 1.0
CA A:LEU287 4.3 36.1 1.0
CB A:LEU286 4.4 39.2 1.0
O A:HOH643 4.4 63.8 1.0
OG1 A:THR199 4.4 34.2 1.0
OH A:TYR239 4.5 39.4 1.0
CD2 A:LEU286 4.8 41.9 1.0
C A:LEU286 4.8 37.5 1.0
CG2 A:THR199 4.9 32.8 1.0
CD1 A:LEU286 4.9 41.0 1.0
CG A:LEU286 5.0 41.1 1.0

Chlorine binding site 3 out of 7 in 7gi3

Go back to Chlorine Binding Sites List in 7gi3
Chlorine binding site 3 out of 7 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 Mat-Pos-090737B9-1 (Mpro-P0041)


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 Mat-Pos-090737B9-1 (Mpro-P0041) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl416

b:77.1
occ:1.00
 O A:HOH507 3.9 41.9 1.0
O A:HOH618 4.1 38.3 1.0
NH2 A:ARG40 4.1 36.6 1.0
O A:HOH597 4.3 28.9 1.0
SG A:CYS85 4.3 37.9 1.0
O A:HOH558 4.6 28.9 1.0
NH1 A:ARG40 4.7 36.6 1.0
CZ A:ARG40 4.7 37.9 1.0
CA A:ASN84 4.8 37.3 1.0
C A:ASN84 4.9 37.1 1.0
OD1 A:ASN84 4.9 41.0 1.0

Chlorine binding site 4 out of 7 in 7gi3

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Chlorine binding site 4 out of 7 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 Mat-Pos-090737B9-1 (Mpro-P0041)


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 Mat-Pos-090737B9-1 (Mpro-P0041) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl417

b:56.1
occ:1.00
 N A:ALA285 3.2 41.5 1.0
N B:ALA285 3.6 42.0 1.0
OG A:SER284 3.6 50.2 1.0
N A:LEU286 3.7 39.2 1.0
OG B:SER284 3.8 46.5 1.0
CA A:ALA285 4.0 41.0 1.0
CB A:ALA285 4.1 41.5 1.0
N B:LEU286 4.1 41.4 1.0
C A:SER284 4.1 42.7 1.0
CA A:SER284 4.1 44.5 1.0
C A:ALA285 4.1 39.8 1.0
CB A:LEU286 4.2 39.2 1.0
CA B:SER284 4.3 42.6 1.0
CG A:LEU286 4.3 41.1 1.0
CB A:SER284 4.3 46.9 1.0
C B:SER284 4.4 42.0 1.0
CA B:ALA285 4.4 42.1 1.0
CG B:LEU286 4.4 43.5 1.0
CB B:LEU286 4.5 41.6 1.0
CB B:SER284 4.5 43.4 1.0
CB B:ALA285 4.5 42.0 1.0
CA A:LEU286 4.6 38.7 1.0
CD1 B:LEU286 4.6 44.3 1.0
C B:ALA285 4.6 42.2 1.0
CD1 A:LEU286 4.7 41.0 1.0
OE2 A:GLU288 4.7 58.0 1.0
CA B:LEU286 4.9 41.1 1.0

Chlorine binding site 5 out of 7 in 7gi3

Go back to Chlorine Binding Sites List in 7gi3
Chlorine binding site 5 out of 7 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 Mat-Pos-090737B9-1 (Mpro-P0041)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 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 Mat-Pos-090737B9-1 (Mpro-P0041) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl418

b:76.5
occ:1.00
 OD1 A:ASN238 3.5 53.3 1.0
O A:LYS236 3.8 42.4 1.0
O A:MET235 4.1 46.0 1.0
C A:LYS236 4.3 42.3 1.0
O A:HOH540 4.3 59.3 1.0
CG A:ASN238 4.5 51.2 1.0
CA A:LYS236 4.5 43.4 1.0
N A:ASN238 4.8 41.9 1.0

Chlorine binding site 6 out of 7 in 7gi3

Go back to Chlorine Binding Sites List in 7gi3
Chlorine binding site 6 out of 7 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 Mat-Pos-090737B9-1 (Mpro-P0041)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 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 Mat-Pos-090737B9-1 (Mpro-P0041) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:57.2
occ:0.80
 CL B:Q0I404 0.0 57.2 0.8
C10 B:Q0I404 1.7 57.6 0.8
C11 B:Q0I404 2.7 57.7 0.8
C9 B:Q0I404 2.7 58.0 0.8
CB B:ASP187 3.3 48.6 1.0
CA B:ASP187 3.4 47.9 1.0
CD2 B:HIS41 3.6 54.0 1.0
CB B:MET165 3.8 46.6 1.0
C B:ASP187 3.8 50.9 1.0
SD B:MET165 3.8 68.4 1.0
O B:HIS164 3.9 41.4 1.0
C12 B:Q0I404 4.0 58.2 0.8
C8 B:Q0I404 4.0 58.5 0.8
NE2 B:HIS41 4.1 55.7 1.0
CG B:MET165 4.1 52.2 1.0
CE B:MET49 4.1 76.7 1.0
N B:ARG188 4.2 53.1 1.0
CG B:HIS41 4.3 52.7 1.0
C B:HIS164 4.3 41.0 1.0
CB B:HIS164 4.3 39.3 1.0
O B:ASP187 4.4 51.2 1.0
O B:HOH513 4.4 35.1 1.0
C7 B:Q0I404 4.5 58.7 0.8
N B:ASP187 4.6 46.2 1.0
O B:VAL186 4.7 45.3 1.0
CG B:ASP187 4.7 51.1 1.0
CB B:HIS41 4.7 50.0 1.0
CZ B:PHE181 4.8 38.8 1.0
N B:MET165 4.8 42.0 1.0
CA B:MET165 4.8 44.2 1.0
CA B:HIS164 4.9 39.1 1.0
CE1 B:HIS41 4.9 56.0 1.0
CD2 B:HIS164 4.9 40.8 1.0

Chlorine binding site 7 out of 7 in 7gi3

Go back to Chlorine Binding Sites List in 7gi3
Chlorine binding site 7 out of 7 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 Mat-Pos-090737B9-1 (Mpro-P0041)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 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 Mat-Pos-090737B9-1 (Mpro-P0041) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:75.6
occ:1.00
 O B:HOH549 3.2 48.6 1.0
O B:PRO132 3.9 34.8 1.0
O B:THR196 4.1 50.3 1.0
C B:PRO132 4.2 34.8 1.0
OG1 B:THR198 4.3 45.0 1.0
O B:HOH540 4.4 48.0 1.0
CB B:PRO132 4.4 35.1 1.0
OE2 B:GLU240 4.5 56.4 1.0
N B:ASN133 4.6 34.3 1.0
CA B:ASN133 4.7 34.3 1.0
CG2 B:THR198 4.8 43.8 1.0
CB B:ASN133 5.0 33.7 1.0
CA B:PRO132 5.0 34.8 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 21:30:36 2024

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