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Sodium in PDB 7i1f: Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group

Enzymatic activity of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group

All present enzymatic activity of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group:
3.4.22.69;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i1f was solved by T.Barthel, L.S.Benz, J.Wollenhaupt, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.78 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.69, 99.33, 103.18, 90, 90, 90
R / Rfree (%) 21.7 / 26

Other elements in 7i1f:

The structure of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group (pdb code 7i1f). 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 Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i1f:

Sodium binding site 1 out of 1 in 7i1f

Go back to Sodium Binding Sites List in 7i1f
Sodium binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment G04 From the F2X-Entry Screen in Orthorhombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:47.3
occ:1.00
 OD1 B:ASP263 1.9 44.8 1.0
OD1 B:ASN221 2.4 41.9 1.0
O B:ASN221 2.5 40.3 1.0
O B:PHE223 2.6 50.7 1.0
O B:ASP263 2.9 36.6 1.0
CG B:ASP263 3.1 49.3 1.0
C B:ASN221 3.4 44.7 1.0
C B:ASP263 3.4 38.3 1.0
CG B:ASN221 3.6 38.1 1.0
CA B:ASP263 3.6 44.6 1.0
C B:PHE223 3.7 47.3 1.0
N B:PHE223 3.7 33.4 1.0
CB B:ASP263 3.9 44.2 1.0
N B:ASN221 4.0 53.3 1.0
CA B:ASN221 4.1 43.6 1.0
OG B:SER267 4.1 49.2 1.0
OD2 B:ASP263 4.1 51.2 1.0
C B:ARG222 4.1 35.1 1.0
N B:ARG222 4.3 41.8 1.0
CA B:PHE223 4.3 37.6 1.0
CB B:ALA266 4.3 48.4 1.0
CB B:ASN221 4.5 44.3 1.0
ND2 B:ASN221 4.5 32.2 1.0
N B:MET264 4.6 43.8 1.0
CA B:ARG222 4.6 40.5 1.0
O B:ARG222 4.7 34.1 1.0
N B:SER267 4.8 47.4 1.0
N B:THR224 4.8 42.2 1.0
CB B:PHE223 5.0 36.0 1.0

Reference:

T.Barthel, J.Wollenhaupt, L.S.Benz, P.Reincke, L.Zhang, F.Lennartz, H.Tabermann, U.Mueller, A.Meente, R.Hilgenfeld, M.S.Weiss. Orthorhombic Sars-Cov-2 Main Protease Crystals Provide Higher Success Rate in Fragment Screening To Be Published.
Page generated: Mon Aug 18 10:11:55 2025

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