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Sodium 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:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 7gnm

Go back to Sodium Binding Sites List in 7gnm
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
B:Na408

b:41.1
occ:1.00
 OD2 B:ASP263 2.2 47.4 1.0
OD1 B:ASN221 2.2 35.6 1.0
O B:PHE223 2.4 30.8 1.0
O B:ASN221 2.5 29.9 1.0
O B:HOH534 2.5 36.1 1.0
O B:ASP263 3.0 32.7 1.0
C B:ASN221 3.3 29.5 1.0
CG B:ASP263 3.3 43.6 1.0
N B:PHE223 3.3 29.0 1.0
CG B:ASN221 3.4 33.5 1.0
C B:PHE223 3.4 31.9 1.0
C B:ASP263 3.7 32.4 1.0
CA B:PHE223 3.8 29.7 1.0
N B:ASN221 3.8 30.1 1.0
CA B:ASP263 3.9 33.7 1.0
CA B:ASN221 3.9 30.2 1.0
CB B:ALA266 3.9 33.9 1.0
C B:ARG222 3.9 29.2 1.0
CB B:ASP263 4.0 37.0 1.0
N B:ARG222 4.1 28.8 1.0
CB B:ASN221 4.2 30.8 1.0
OD1 B:ASP263 4.3 43.3 1.0
ND2 B:ASN221 4.4 33.6 1.0
OG B:SER267 4.4 36.4 1.0
CA B:ARG222 4.4 28.4 1.0
N B:SER267 4.5 32.3 1.0
CB B:PHE223 4.5 28.7 1.0
N B:THR224 4.6 34.2 1.0
O B:ARG222 4.7 29.1 1.0
N B:MET264 4.9 30.4 1.0
C B:ALA266 4.9 33.2 1.0
CA B:ALA266 4.9 33.7 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: Tue Oct 8 16:51:47 2024

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