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Bromine in PDB 7i1d: Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment F04 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 F04 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 F04 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 F04 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i1d 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) 46.06 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.96, 99.47, 103.93, 90, 90, 90
R / Rfree (%) 22.6 / 26.8

Other elements in 7i1d:

The structure of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment F04 From the F2X-Entry Screen in Orthorhombic Space Group also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment F04 From the F2X-Entry Screen in Orthorhombic Space Group (pdb code 7i1d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment F04 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i1d:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 7i1d

Go back to Bromine Binding Sites List in 7i1d
Bromine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment F04 From the F2X-Entry Screen in Orthorhombic Space Group


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment F04 From the F2X-Entry Screen in Orthorhombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br402

b:42.7
occ:0.30
 BR A:RB7402 0.0 42.7 0.3
BR A:RB7402 0.0 42.7 0.3
C6 A:RB7402 1.9 40.4 0.3
C6 A:RB7402 1.9 40.4 0.3
C5 A:RB7402 2.9 40.6 0.3
C5 A:RB7402 2.9 40.6 0.3
C1 A:RB7402 2.9 37.5 0.3
C1 A:RB7402 2.9 37.5 0.3
C A:RB7402 3.2 34.4 0.3
C A:RB7402 3.2 34.4 0.3
C A:ASP187 3.7 25.1 0.2
C A:ASP187 3.7 25.1 0.2
CA A:ASP187 3.8 24.3 0.2
CA A:ASP187 3.8 24.3 0.2
CA A:ASP187 3.8 24.9 0.3
CA A:ASP187 3.8 24.9 0.3
SD A:MET165 3.8 28.9 0.2
SD A:MET165 3.8 28.9 0.2
C A:ASP187 3.9 26.1 0.3
C A:ASP187 3.9 26.1 0.3
SD A:MET165 3.9 33.1 0.3
SD A:MET165 3.9 33.1 0.3
N A:ARG188 4.0 26.1 0.2
N A:ARG188 4.0 26.1 0.2
CD2 A:HIS41 4.1 23.8 0.2
CD2 A:HIS41 4.1 23.8 0.2
CB A:ASP187 4.1 24.2 0.3
CB A:ASP187 4.1 24.2 0.3
CG A:GLN189 4.1 43.5 0.3
CG A:GLN189 4.1 43.5 0.3
N A:ARG188 4.1 27.9 0.3
N A:ARG188 4.1 27.9 0.3
O A:ASP187 4.1 24.6 0.2
O A:ASP187 4.1 24.6 0.2
CB A:ASP187 4.1 23.7 0.2
CB A:ASP187 4.1 23.7 0.2
NE2 A:GLN189 4.2 46.5 0.3
NE2 A:GLN189 4.2 46.5 0.3
C4 A:RB7402 4.2 42.9 0.3
C4 A:RB7402 4.2 42.9 0.3
CB A:MET165 4.2 26.5 0.3
CB A:MET165 4.2 26.5 0.3
C2 A:RB7402 4.2 41.9 0.3
C2 A:RB7402 4.2 41.9 0.3
CB A:MET165 4.3 24.6 0.2
CB A:MET165 4.3 24.6 0.2
O A:ASP187 4.3 25.6 0.3
O A:ASP187 4.3 25.6 0.3
CD2 A:HIS41 4.4 25.0 0.3
CD2 A:HIS41 4.4 25.0 0.3
CG A:HIS41 4.5 23.6 0.2
CG A:HIS41 4.5 23.6 0.2
CG A:MET165 4.5 28.7 0.3
CG A:MET165 4.5 28.7 0.3
C A:ARG188 4.5 28.4 0.2
C A:ARG188 4.5 28.4 0.2
C A:ARG188 4.5 30.1 0.3
C A:ARG188 4.5 30.1 0.3
CG A:GLN189 4.6 39.3 0.2
CG A:GLN189 4.6 39.3 0.2
CA A:ARG188 4.6 27.3 0.2
CA A:ARG188 4.6 27.3 0.2
O A:ARG188 4.6 26.5 0.2
O A:ARG188 4.6 26.5 0.2
CG A:MET165 4.6 25.8 0.2
CG A:MET165 4.6 25.8 0.2
O A:ARG188 4.6 26.9 0.3
O A:ARG188 4.6 26.9 0.3
CG A:HIS41 4.6 24.4 0.3
CG A:HIS41 4.6 24.4 0.3
O A:HIS164 4.6 21.5 0.2
O A:HIS164 4.6 21.5 0.2
CD A:GLN189 4.6 47.2 0.3
CD A:GLN189 4.6 47.2 0.3
CB A:HIS41 4.7 24.2 0.3
CB A:HIS41 4.7 24.2 0.3
CB A:HIS41 4.7 23.6 0.2
CB A:HIS41 4.7 23.6 0.2
NE2 A:HIS41 4.7 23.9 0.2
NE2 A:HIS41 4.7 23.9 0.2
CA A:ARG188 4.7 29.6 0.3
CA A:ARG188 4.7 29.6 0.3
C3 A:RB7402 4.8 44.9 0.3
C3 A:RB7402 4.8 44.9 0.3
N A:GLN189 4.8 31.4 0.2
N A:GLN189 4.8 31.4 0.2
N A:GLN189 4.9 33.1 0.3
N A:GLN189 4.9 33.1 0.3
O A:VAL186 4.9 23.1 1.0
O A:HIS164 5.0 22.9 0.3
O A:HIS164 5.0 22.9 0.3

Bromine binding site 2 out of 2 in 7i1d

Go back to Bromine Binding Sites List in 7i1d
Bromine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment F04 From the F2X-Entry Screen in Orthorhombic Space Group


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment F04 From the F2X-Entry Screen in Orthorhombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br402

b:42.7
occ:0.30
 BR A:RB7402 0.0 42.7 0.3
BR A:RB7402 0.0 42.7 0.3
C6 A:RB7402 1.9 40.4 0.3
C6 A:RB7402 1.9 40.4 0.3
C5 A:RB7402 2.9 40.6 0.3
C5 A:RB7402 2.9 40.6 0.3
C1 A:RB7402 2.9 37.5 0.3
C1 A:RB7402 2.9 37.5 0.3
C A:RB7402 3.2 34.4 0.3
C A:RB7402 3.2 34.4 0.3
C A:ASP187 3.7 25.1 0.2
C A:ASP187 3.7 25.1 0.2
CA A:ASP187 3.8 24.3 0.2
CA A:ASP187 3.8 24.3 0.2
CA A:ASP187 3.8 24.9 0.3
CA A:ASP187 3.8 24.9 0.3
SD A:MET165 3.8 28.9 0.2
SD A:MET165 3.8 28.9 0.2
C A:ASP187 3.9 26.1 0.3
C A:ASP187 3.9 26.1 0.3
SD A:MET165 3.9 33.1 0.3
SD A:MET165 3.9 33.1 0.3
N A:ARG188 4.0 26.1 0.2
N A:ARG188 4.0 26.1 0.2
CD2 A:HIS41 4.1 23.8 0.2
CD2 A:HIS41 4.1 23.8 0.2
CB A:ASP187 4.1 24.2 0.3
CB A:ASP187 4.1 24.2 0.3
CG A:GLN189 4.1 43.5 0.3
CG A:GLN189 4.1 43.5 0.3
N A:ARG188 4.1 27.9 0.3
N A:ARG188 4.1 27.9 0.3
O A:ASP187 4.1 24.6 0.2
O A:ASP187 4.1 24.6 0.2
CB A:ASP187 4.1 23.7 0.2
CB A:ASP187 4.1 23.7 0.2
NE2 A:GLN189 4.2 46.5 0.3
NE2 A:GLN189 4.2 46.5 0.3
C4 A:RB7402 4.2 42.9 0.3
C4 A:RB7402 4.2 42.9 0.3
CB A:MET165 4.2 26.5 0.3
CB A:MET165 4.2 26.5 0.3
C2 A:RB7402 4.2 41.9 0.3
C2 A:RB7402 4.2 41.9 0.3
CB A:MET165 4.3 24.6 0.2
CB A:MET165 4.3 24.6 0.2
O A:ASP187 4.3 25.6 0.3
O A:ASP187 4.3 25.6 0.3
CD2 A:HIS41 4.4 25.0 0.3
CD2 A:HIS41 4.4 25.0 0.3
CG A:HIS41 4.5 23.6 0.2
CG A:HIS41 4.5 23.6 0.2
CG A:MET165 4.5 28.7 0.3
CG A:MET165 4.5 28.7 0.3
C A:ARG188 4.5 28.4 0.2
C A:ARG188 4.5 28.4 0.2
C A:ARG188 4.5 30.1 0.3
C A:ARG188 4.5 30.1 0.3
CG A:GLN189 4.6 39.3 0.2
CG A:GLN189 4.6 39.3 0.2
CA A:ARG188 4.6 27.3 0.2
CA A:ARG188 4.6 27.3 0.2
O A:ARG188 4.6 26.5 0.2
O A:ARG188 4.6 26.5 0.2
CG A:MET165 4.6 25.8 0.2
CG A:MET165 4.6 25.8 0.2
O A:ARG188 4.6 26.9 0.3
O A:ARG188 4.6 26.9 0.3
CG A:HIS41 4.6 24.4 0.3
CG A:HIS41 4.6 24.4 0.3
O A:HIS164 4.6 21.5 0.2
O A:HIS164 4.6 21.5 0.2
CD A:GLN189 4.6 47.2 0.3
CD A:GLN189 4.6 47.2 0.3
CB A:HIS41 4.7 24.2 0.3
CB A:HIS41 4.7 24.2 0.3
CB A:HIS41 4.7 23.6 0.2
CB A:HIS41 4.7 23.6 0.2
NE2 A:HIS41 4.7 23.9 0.2
NE2 A:HIS41 4.7 23.9 0.2
CA A:ARG188 4.7 29.6 0.3
CA A:ARG188 4.7 29.6 0.3
C3 A:RB7402 4.8 44.9 0.3
C3 A:RB7402 4.8 44.9 0.3
N A:GLN189 4.8 31.4 0.2
N A:GLN189 4.8 31.4 0.2
N A:GLN189 4.9 33.1 0.3
N A:GLN189 4.9 33.1 0.3
O A:VAL186 4.9 23.1 1.0
O A:HIS164 5.0 22.9 0.3
O A:HIS164 5.0 22.9 0.3

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 Jul 7 11:22:53 2025

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