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

Go back to Fluorine Binding Sites List in 8ign
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

Go back to Fluorine Binding Sites List in 8ign
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

Go back to Fluorine Binding Sites List in 8ign
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy