Atomistry » Sodium » PDB 7grf-7ick » 7i17
Atomistry »
  Sodium »
    PDB 7grf-7ick »
      7i17 »

Sodium in PDB 7i17: Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment C10 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 C10 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 C10 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 C10 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i17 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) 46.00 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.89, 99.84, 103.65, 90, 90, 90
R / Rfree (%) 23 / 26

Other elements in 7i17:

The structure of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment C10 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 C10 From the F2X-Entry Screen in Orthorhombic Space Group (pdb code 7i17). 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 C10 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i17:

Sodium binding site 1 out of 1 in 7i17

Go back to Sodium Binding Sites List in 7i17
Sodium binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment C10 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 C10 From the F2X-Entry Screen in Orthorhombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:46.1
occ:1.00
 OD1 B:ASP263 1.8 38.1 1.0
OD1 B:ASN221 2.4 39.7 1.0
O B:ASN221 2.7 46.5 1.0
CG B:ASP263 2.9 41.8 1.0
O B:PHE223 2.9 51.5 1.0
O B:ASP263 3.0 35.7 1.0
C B:ASP263 3.3 34.0 1.0
CA B:ASP263 3.4 37.8 1.0
C B:ASN221 3.5 46.4 1.0
CB B:ASP263 3.5 40.6 1.0
CG B:ASN221 3.6 40.0 1.0
C B:PHE223 3.9 54.3 1.0
N B:PHE223 3.9 35.5 1.0
OD2 B:ASP263 4.0 44.4 1.0
OG B:SER267 4.0 53.6 1.0
N B:ASN221 4.0 52.2 1.0
CA B:ASN221 4.2 45.2 1.0
N B:MET264 4.3 40.3 1.0
C B:ARG222 4.3 37.3 1.0
N B:ARG222 4.4 43.2 1.0
CA B:PHE223 4.5 40.3 1.0
CB B:ALA266 4.5 52.5 1.0
CB B:ASN221 4.5 44.3 1.0
ND2 B:ASN221 4.5 30.4 1.0
CA B:ARG222 4.8 43.4 1.0
CG2 B:ILE259 4.8 32.7 1.0
N B:ASP263 4.8 35.1 1.0
N B:THR224 4.9 54.7 1.0
N B:SER267 4.9 49.0 1.0
O B:ARG222 5.0 35.0 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 10:11:38 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy