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Fluorine in PDB 8ign: Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216, PDB code: 8ign was solved by X.Huang, B.Zhou, J.Xu, Z.Yang, N.Zhong, X.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.47 / 2.02
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.829, 60.935, 64.037, 80.03, 68.34, 70.67
R / Rfree (%) 18.6 / 23.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216 (pdb code 8ign). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216, PDB code: 8ign:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8ign

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Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.3
occ:1.00
 F1 B:7ON401 0.0 40.3 1.0
C31 B:7ON401 1.3 37.5 1.0
F2 B:7ON401 2.1 45.4 1.0
F3 B:7ON401 2.1 44.2 1.0
C30 B:7ON401 2.4 35.7 1.0
O5 B:7ON401 2.9 35.6 1.0
O B:THR190 3.2 40.3 1.0
N5 B:7ON401 3.3 31.4 1.0
N B:GLN192 3.8 38.9 1.0
O B:HOH571 3.9 52.8 1.0
O B:GLN192 4.1 41.7 1.0
C B:THR190 4.2 42.4 1.0
CG B:PRO168 4.4 37.8 1.0
CD B:PRO168 4.4 35.5 1.0
O B:HOH564 4.4 46.6 1.0
CA B:ALA191 4.5 44.1 1.0
CB B:GLN192 4.6 34.1 1.0
C B:ALA191 4.6 43.4 1.0
O B:GLU166 4.6 25.2 1.0
C18 B:7ON401 4.6 31.5 1.0
CA B:GLN192 4.6 38.4 1.0
N B:ALA191 4.7 43.7 1.0
CD2 B:LEU167 4.7 33.4 1.0
CG B:GLN192 4.8 31.3 1.0
C B:GLN192 4.8 40.6 1.0
C20 B:7ON401 4.8 47.8 1.0
NE2 B:GLN192 4.8 29.8 1.0
CE B:MET165 5.0 35.5 1.0
N B:THR190 5.0 40.5 1.0

Fluorine binding site 2 out of 6 in 8ign

Go back to Fluorine Binding Sites List in 8ign
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:45.4
occ:1.00
 F2 B:7ON401 0.0 45.4 1.0
C31 B:7ON401 1.3 37.5 1.0
F1 B:7ON401 2.1 40.3 1.0
F3 B:7ON401 2.1 44.2 1.0
C30 B:7ON401 2.4 35.7 1.0
N5 B:7ON401 2.6 31.4 1.0
O B:GLU166 3.0 25.2 1.0
CE B:MET165 3.4 35.5 1.0
CD2 B:LEU167 3.4 33.4 1.0
O5 B:7ON401 3.5 35.6 1.0
CA B:LEU167 3.7 26.6 1.0
C B:GLU166 3.9 24.6 1.0
C18 B:7ON401 4.1 31.5 1.0
CG B:LEU167 4.1 29.2 1.0
N B:LEU167 4.2 24.6 1.0
O B:HOH564 4.2 46.6 1.0
CD B:PRO168 4.3 35.5 1.0
CB B:LEU167 4.5 27.7 1.0
O B:GLN192 4.5 41.7 1.0
NE2 B:GLN192 4.5 29.8 1.0
CB B:GLN192 4.6 34.1 1.0
O B:THR190 4.6 40.3 1.0
C B:LEU167 4.7 29.8 1.0
C17 B:7ON401 4.7 31.6 1.0
N B:PRO168 4.8 34.6 1.0
C19 B:7ON401 4.8 39.0 1.0
CD B:GLN192 4.9 28.3 1.0
SD B:MET165 4.9 40.1 1.0
N B:GLN192 5.0 38.9 1.0
CG B:GLN192 5.0 31.3 1.0
CG B:PRO168 5.0 37.8 1.0

Fluorine binding site 3 out of 6 in 8ign

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Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:44.2
occ:1.00
 F3 B:7ON401 0.0 44.2 1.0
C31 B:7ON401 1.3 37.5 1.0
F2 B:7ON401 2.1 45.4 1.0
F1 B:7ON401 2.1 40.3 1.0
C30 B:7ON401 2.4 35.7 1.0
O5 B:7ON401 2.8 35.6 1.0
NE2 B:GLN192 2.9 29.8 1.0
O B:THR190 2.9 40.3 1.0
CE B:MET165 3.2 35.5 1.0
N5 B:7ON401 3.4 31.4 1.0
CD B:GLN192 3.5 28.3 1.0
CG B:GLN192 3.6 31.3 1.0
O B:ARG188 3.8 29.0 1.0
CB B:GLN192 3.9 34.1 1.0
C B:THR190 4.1 42.4 1.0
N B:GLN192 4.2 38.9 1.0
N B:THR190 4.2 40.5 1.0
O B:HOH571 4.4 52.8 1.0
OE1 B:GLN192 4.5 28.3 1.0
CA B:GLN192 4.6 38.4 1.0
C18 B:7ON401 4.7 31.5 1.0
CD2 B:LEU167 4.7 33.4 1.0
CA B:THR190 4.8 43.5 1.0
C B:ALA191 4.9 43.4 1.0
SD B:MET165 4.9 40.1 1.0
CA B:GLN189 4.9 37.9 1.0
C B:ARG188 4.9 31.5 1.0
O B:GLU166 4.9 25.2 1.0
O B:GLN192 5.0 41.7 1.0

Fluorine binding site 4 out of 6 in 8ign

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Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:49.1
occ:1.00
 F1 A:7ON401 0.0 49.1 1.0
C31 A:7ON401 1.3 44.9 1.0
F2 A:7ON401 2.1 43.5 1.0
F3 A:7ON401 2.1 54.8 1.0
C30 A:7ON401 2.4 44.8 1.0
O5 A:7ON401 3.0 46.9 1.0
N5 A:7ON401 3.2 40.1 1.0
O A:THR190 3.3 54.0 1.0
N A:GLN192 3.9 49.0 1.0
O A:GLN192 4.1 52.1 1.0
C A:THR190 4.3 56.4 1.0
CD A:PRO168 4.3 49.8 1.0
CG A:PRO168 4.3 51.3 1.0
CB A:GLN192 4.5 46.0 1.0
O A:GLU166 4.5 34.3 1.0
C18 A:7ON401 4.5 42.0 1.0
CA A:ALA191 4.6 56.0 1.0
CA A:GLN192 4.6 49.1 1.0
CG A:GLN192 4.6 44.4 1.0
C A:ALA191 4.7 54.3 1.0
CD2 A:LEU167 4.7 44.1 1.0
C20 A:7ON401 4.8 63.7 1.0
C A:GLN192 4.8 54.1 1.0
N A:ALA191 4.8 55.6 1.0
NE2 A:GLN192 4.9 41.0 1.0
CA A:LEU167 5.0 40.5 1.0
CE A:MET165 5.0 52.0 1.0

Fluorine binding site 5 out of 6 in 8ign

Go back to Fluorine Binding Sites List in 8ign
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:43.5
occ:1.00
 F2 A:7ON401 0.0 43.5 1.0
C31 A:7ON401 1.3 44.9 1.0
F3 A:7ON401 2.1 54.8 1.0
F1 A:7ON401 2.1 49.1 1.0
C30 A:7ON401 2.4 44.8 1.0
N5 A:7ON401 2.6 40.1 1.0
O A:GLU166 3.1 34.3 1.0
CD2 A:LEU167 3.3 44.1 1.0
CE A:MET165 3.4 52.0 1.0
O5 A:7ON401 3.5 46.9 1.0
CA A:LEU167 3.8 40.5 1.0
C A:GLU166 3.9 36.4 1.0
C18 A:7ON401 4.1 42.0 1.0
N A:LEU167 4.2 38.2 1.0
CG A:LEU167 4.2 43.0 1.0
CD A:PRO168 4.5 49.8 1.0
CB A:LEU167 4.5 40.5 1.0
CB A:GLN192 4.5 46.0 1.0
NE2 A:GLN192 4.6 41.0 1.0
O A:GLN192 4.7 52.1 1.0
SD A:MET165 4.7 53.7 1.0
O A:THR190 4.7 54.0 1.0
C17 A:7ON401 4.7 43.7 1.0
C A:LEU167 4.8 42.4 1.0
CD A:GLN192 4.8 39.8 1.0
CG A:GLN192 4.8 44.4 1.0
C19 A:7ON401 4.9 52.3 1.0
CB A:MET165 4.9 39.1 1.0
N A:PRO168 4.9 45.5 1.0
CG A:MET165 5.0 40.7 1.0

Fluorine binding site 6 out of 6 in 8ign

Go back to Fluorine Binding Sites List in 8ign
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with RAY1216 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:54.8
occ:1.00
 F3 A:7ON401 0.0 54.8 1.0
C31 A:7ON401 1.3 44.9 1.0
F2 A:7ON401 2.1 43.5 1.0
F1 A:7ON401 2.1 49.1 1.0
C30 A:7ON401 2.4 44.8 1.0
O5 A:7ON401 2.8 46.9 1.0
O A:THR190 2.9 54.0 1.0
NE2 A:GLN192 2.9 41.0 1.0
CE A:MET165 3.3 52.0 1.0
CD A:GLN192 3.4 39.8 1.0
N5 A:7ON401 3.5 40.1 1.0
CG A:GLN192 3.5 44.4 1.0
O A:ARG188 3.8 43.3 1.0
CB A:GLN192 3.8 46.0 1.0
C A:THR190 4.0 56.4 1.0
N A:THR190 4.1 51.5 1.0
N A:GLN192 4.2 49.0 1.0
OE1 A:GLN192 4.4 36.4 1.0
CA A:GLN192 4.6 49.1 1.0
CD2 A:LEU167 4.7 44.1 1.0
C18 A:7ON401 4.7 42.0 1.0
CA A:THR190 4.8 55.8 1.0
CA A:GLN189 4.8 46.4 1.0
C A:ARG188 4.8 43.3 1.0
SD A:MET165 4.9 53.7 1.0
C A:ALA191 4.9 54.3 1.0
C A:GLN189 5.0 49.5 1.0

Reference:

X.Huang, B.Zhou, X.Xiong, Z.Yang. Inhibition Mechanism and Antiviral Activity of An Alpha-Ketoamide Based Sars-Cov-2 Main Protease Inhibitor To Be Published.
Page generated: Fri Aug 2 20:43:52 2024

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