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Fluorine in PDB 7i18: Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 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 D04 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 D04 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 D04 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i18 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) 45.89 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.05, 99.28, 103.5, 90, 90, 90
R / Rfree (%) 21 / 25.5

Other elements in 7i18:

The structure of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group (pdb code 7i18). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i18:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7i18

Go back to Fluorine Binding Sites List in 7i18
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:32.4
occ:0.25
F A:R9D501 0.0 32.4 0.2
F A:R9D501 0.0 32.4 0.2
C7 A:R9D501 1.4 32.1 0.2
C7 A:R9D501 1.4 32.1 0.2
C8 A:R9D501 2.3 31.9 0.2
C8 A:R9D501 2.3 31.9 0.2
C6 A:R9D501 2.4 31.2 0.2
C6 A:R9D501 2.4 31.2 0.2
C A:ASP187 3.0 26.6 0.2
C A:ASP187 3.0 26.6 0.2
C A:ASP187 3.0 27.3 0.2
C A:ASP187 3.0 27.3 0.2
CA A:ASP187 3.1 26.2 0.2
CA A:ASP187 3.1 26.2 0.2
CA A:ASP187 3.1 26.7 0.2
CA A:ASP187 3.1 26.7 0.2
O A:ASP187 3.3 26.2 0.2
O A:ASP187 3.3 26.2 0.2
N A:ARG188 3.3 27.9 0.2
N A:ARG188 3.3 27.9 0.2
N A:ARG188 3.4 27.0 0.2
N A:ARG188 3.4 27.0 0.2
CB A:ASP187 3.5 25.4 0.2
CB A:ASP187 3.5 25.4 0.2
O A:ASP187 3.5 26.7 0.2
O A:ASP187 3.5 26.7 0.2
CB A:ASP187 3.6 26.0 0.2
CB A:ASP187 3.6 26.0 0.2
C9 A:R9D501 3.6 32.1 0.2
C9 A:R9D501 3.6 32.1 0.2
C5 A:R9D501 3.6 33.1 0.2
C5 A:R9D501 3.6 33.1 0.2
CD2 A:HIS41 3.8 24.8 0.2
CD2 A:HIS41 3.8 24.8 0.2
CA A:ARG188 4.0 29.9 0.2
CA A:ARG188 4.0 29.9 0.2
CA A:ARG188 4.1 28.6 0.2
CA A:ARG188 4.1 28.6 0.2
C4 A:R9D501 4.1 33.7 0.2
C4 A:R9D501 4.1 33.7 0.2
CG A:HIS41 4.2 25.0 0.2
CG A:HIS41 4.2 25.0 0.2
C A:ARG188 4.2 30.3 0.2
C A:ARG188 4.2 30.3 0.2
CB A:HIS41 4.3 25.4 0.2
CB A:HIS41 4.3 25.4 0.2
C A:ARG188 4.3 28.9 0.2
C A:ARG188 4.3 28.9 0.2
SD A:MET165 4.3 34.5 0.2
SD A:MET165 4.3 34.5 0.2
NE2 A:GLN189 4.3 41.4 0.2
NE2 A:GLN189 4.3 41.4 0.2
CB A:HIS41 4.4 30.6 0.2
CB A:HIS41 4.4 30.6 0.2
CG A:HIS41 4.4 31.3 0.2
CG A:HIS41 4.4 31.3 0.2
CD2 A:HIS41 4.5 32.9 0.2
CD2 A:HIS41 4.5 32.9 0.2
N A:ASP187 4.5 26.1 0.2
N A:ASP187 4.5 26.1 0.2
SD A:MET165 4.5 36.4 0.2
SD A:MET165 4.5 36.4 0.2
N A:ASP187 4.5 26.5 0.2
N A:ASP187 4.5 26.5 0.2
O A:ARG188 4.5 29.2 0.2
O A:ARG188 4.5 29.2 0.2
CG A:GLN189 4.6 40.5 0.2
CG A:GLN189 4.6 40.5 0.2
O A:ARG188 4.6 27.6 0.2
O A:ARG188 4.6 27.6 0.2
OH A:TYR54 4.6 27.5 0.2
OH A:TYR54 4.6 27.5 0.2
OH A:TYR54 4.6 27.4 0.2
OH A:TYR54 4.6 27.4 0.2
O A:VAL186 4.6 25.9 1.0
NE2 A:HIS41 4.7 26.0 0.2
NE2 A:HIS41 4.7 26.0 0.2
CG A:ASP187 4.8 25.3 0.2
CG A:ASP187 4.8 25.3 0.2
CE A:MET49 4.8 64.8 0.2
CE A:MET49 4.8 64.8 0.2
N A:GLN189 4.8 33.0 0.2
N A:GLN189 4.8 33.0 0.2
N A:GLN189 4.8 31.8 0.2
N A:GLN189 4.8 31.8 0.2
CG A:ASP187 4.9 26.1 0.2
CG A:ASP187 4.9 26.1 0.2
CB A:MET165 4.9 30.9 0.2
CB A:MET165 4.9 30.9 0.2
CB A:MET165 5.0 29.5 0.2
CB A:MET165 5.0 29.5 0.2

Fluorine binding site 2 out of 2 in 7i18

Go back to Fluorine Binding Sites List in 7i18
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:32.4
occ:0.25
F A:R9D501 0.0 32.4 0.2
F A:R9D501 0.0 32.4 0.2
C7 A:R9D501 1.4 32.1 0.2
C7 A:R9D501 1.4 32.1 0.2
C8 A:R9D501 2.3 31.9 0.2
C8 A:R9D501 2.3 31.9 0.2
C6 A:R9D501 2.4 31.2 0.2
C6 A:R9D501 2.4 31.2 0.2
C A:ASP187 3.0 26.6 0.2
C A:ASP187 3.0 26.6 0.2
C A:ASP187 3.0 27.3 0.2
C A:ASP187 3.0 27.3 0.2
CA A:ASP187 3.1 26.2 0.2
CA A:ASP187 3.1 26.2 0.2
CA A:ASP187 3.1 26.7 0.2
CA A:ASP187 3.1 26.7 0.2
O A:ASP187 3.3 26.2 0.2
O A:ASP187 3.3 26.2 0.2
N A:ARG188 3.3 27.9 0.2
N A:ARG188 3.3 27.9 0.2
N A:ARG188 3.4 27.0 0.2
N A:ARG188 3.4 27.0 0.2
CB A:ASP187 3.5 25.4 0.2
CB A:ASP187 3.5 25.4 0.2
O A:ASP187 3.5 26.7 0.2
O A:ASP187 3.5 26.7 0.2
CB A:ASP187 3.6 26.0 0.2
CB A:ASP187 3.6 26.0 0.2
C9 A:R9D501 3.6 32.1 0.2
C9 A:R9D501 3.6 32.1 0.2
C5 A:R9D501 3.6 33.1 0.2
C5 A:R9D501 3.6 33.1 0.2
CD2 A:HIS41 3.8 24.8 0.2
CD2 A:HIS41 3.8 24.8 0.2
CA A:ARG188 4.0 29.9 0.2
CA A:ARG188 4.0 29.9 0.2
CA A:ARG188 4.1 28.6 0.2
CA A:ARG188 4.1 28.6 0.2
C4 A:R9D501 4.1 33.7 0.2
C4 A:R9D501 4.1 33.7 0.2
CG A:HIS41 4.2 25.0 0.2
CG A:HIS41 4.2 25.0 0.2
C A:ARG188 4.2 30.3 0.2
C A:ARG188 4.2 30.3 0.2
CB A:HIS41 4.3 25.4 0.2
CB A:HIS41 4.3 25.4 0.2
C A:ARG188 4.3 28.9 0.2
C A:ARG188 4.3 28.9 0.2
SD A:MET165 4.3 34.5 0.2
SD A:MET165 4.3 34.5 0.2
NE2 A:GLN189 4.3 41.4 0.2
NE2 A:GLN189 4.3 41.4 0.2
CB A:HIS41 4.4 30.6 0.2
CB A:HIS41 4.4 30.6 0.2
CG A:HIS41 4.4 31.3 0.2
CG A:HIS41 4.4 31.3 0.2
CD2 A:HIS41 4.5 32.9 0.2
CD2 A:HIS41 4.5 32.9 0.2
N A:ASP187 4.5 26.1 0.2
N A:ASP187 4.5 26.1 0.2
SD A:MET165 4.5 36.4 0.2
SD A:MET165 4.5 36.4 0.2
N A:ASP187 4.5 26.5 0.2
N A:ASP187 4.5 26.5 0.2
O A:ARG188 4.5 29.2 0.2
O A:ARG188 4.5 29.2 0.2
CG A:GLN189 4.6 40.5 0.2
CG A:GLN189 4.6 40.5 0.2
O A:ARG188 4.6 27.6 0.2
O A:ARG188 4.6 27.6 0.2
OH A:TYR54 4.6 27.5 0.2
OH A:TYR54 4.6 27.5 0.2
OH A:TYR54 4.6 27.4 0.2
OH A:TYR54 4.6 27.4 0.2
O A:VAL186 4.6 25.9 1.0
NE2 A:HIS41 4.7 26.0 0.2
NE2 A:HIS41 4.7 26.0 0.2
CG A:ASP187 4.8 25.3 0.2
CG A:ASP187 4.8 25.3 0.2
CE A:MET49 4.8 64.8 0.2
CE A:MET49 4.8 64.8 0.2
N A:GLN189 4.8 33.0 0.2
N A:GLN189 4.8 33.0 0.2
N A:GLN189 4.8 31.8 0.2
N A:GLN189 4.8 31.8 0.2
CG A:ASP187 4.9 26.1 0.2
CG A:ASP187 4.9 26.1 0.2
CB A:MET165 4.9 30.9 0.2
CB A:MET165 4.9 30.9 0.2
CB A:MET165 5.0 29.5 0.2
CB A:MET165 5.0 29.5 0.2

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: Tue Jul 15 20:24:31 2025

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