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Sodium in PDB 7grf: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2, PDB code: 7grf was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.68 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.71, 99.47, 103.64, 90, 90, 90
R / Rfree (%) 19.7 / 23.9

Other elements in 7grf:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2 also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2 (pdb code 7grf). 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 Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2, PDB code: 7grf:

Sodium binding site 1 out of 1 in 7grf

Go back to Sodium Binding Sites List in 7grf
Sodium binding site 1 out of 1 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:27.0
occ:1.00
 OD1 B:ASP263 2.1 35.5 1.0
OD1 B:ASN221 2.2 24.0 1.0
O B:HOH510 2.3 22.5 1.0
O B:PHE223 2.4 23.2 1.0
O B:ASN221 2.6 21.5 1.0
O B:ASP263 2.9 27.1 1.0
C B:ASN221 3.3 25.8 1.0
CG B:ASN221 3.4 24.3 1.0
CG B:ASP263 3.4 38.9 1.0
C B:PHE223 3.4 21.9 1.0
N B:PHE223 3.4 17.3 1.0
C B:ASP263 3.7 30.9 1.0
N B:ASN221 3.8 29.8 1.0
CB B:ALA266 3.9 30.0 1.0
CA B:PHE223 4.0 24.5 1.0
CA B:ASN221 4.0 21.4 1.0
C B:ARG222 4.0 17.7 1.0
CA B:ASP263 4.1 35.5 1.0
OG B:SER267 4.2 26.4 1.0
N B:ARG222 4.2 23.7 1.0
OD2 B:ASP263 4.2 34.4 1.0
CB B:ASN221 4.3 18.1 1.0
ND2 B:ASN221 4.3 22.1 1.0
CB B:ASP263 4.3 30.9 1.0
N B:SER267 4.5 24.1 1.0
CA B:ARG222 4.5 20.3 1.0
N B:THR224 4.6 23.1 1.0
CB B:PHE223 4.6 20.5 1.0
O B:ARG222 4.7 20.7 1.0
N B:MET264 4.9 25.3 1.0
C B:ALA266 4.9 23.0 1.0
CA B:ALA266 4.9 30.4 1.0
CA B:THR224 5.0 29.7 1.0

Reference:

C.Y.Huang, A.Metz, R.Lange, N.Artico, C.Potot, J.Hazemann, M.Muller, M.Dos Santos, A.Chambovey, D.Ritz, D.Eris, S.Meyer, G.Bourquin, M.Sharpe, A.Mac Sweeney. Fragment-Based Screening Targeting An Open Form of the Sars-Cov-2 Main Protease Binding Pocket. Acta Crystallogr D Struct V. 80 123 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38289714
DOI: 10.1107/S2059798324000329
Page generated: Mon Aug 18 10:09:34 2025

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