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Fluorine in PDB 8dz0: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir

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

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

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir, PDB code: 8dz0 was solved by G.D.Noske, G.Oliva, A.S.Godoy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.42 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.914, 99.018, 103.104, 90, 90, 90
R / Rfree (%) 21.9 / 27.5

Other elements in 8dz0:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir (pdb code 8dz0). 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 Ensitrelvir, PDB code: 8dz0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8dz0

Go back to Fluorine Binding Sites List in 8dz0
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir


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 Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:66.8
occ:1.00
 F28 A:7YY403 0.0 66.8 1.0
C27 A:7YY403 1.4 57.9 1.0
C29 A:7YY403 2.4 54.0 1.0
C26 A:7YY403 2.4 45.9 1.0
NE2 A:GLN189 2.6 72.6 1.0
C25 A:7YY403 2.8 47.6 1.0
CD A:GLN189 3.1 61.6 1.0
OE1 A:GLN189 3.6 56.8 1.0
C30 A:7YY403 3.6 46.9 1.0
C34 A:7YY403 3.6 50.9 1.0
CG A:GLN189 3.7 69.1 1.0
C32 A:7YY403 4.1 57.3 1.0
N24 A:7YY403 4.2 43.9 1.0
O A:HOH527 4.2 31.6 1.0
O A:ARG188 4.4 56.0 1.0
CA A:GLN189 4.5 48.4 1.0
O36 A:7YY403 4.5 45.7 1.0
CB A:GLN189 4.6 61.1 1.0
CB A:MET165 4.6 35.0 1.0
F31 A:7YY403 4.7 51.6 1.0
N A:GLN189 4.9 51.4 1.0
C A:ARG188 4.9 47.2 1.0
C35 A:7YY403 4.9 40.7 1.0

Fluorine binding site 2 out of 6 in 8dz0

Go back to Fluorine Binding Sites List in 8dz0
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir


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 Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:51.6
occ:1.00
 F31 A:7YY403 0.0 51.6 1.0
C30 A:7YY403 1.4 46.9 1.0
C29 A:7YY403 2.4 54.0 1.0
C32 A:7YY403 2.4 57.3 1.0
F33 A:7YY403 2.8 53.8 1.0
C A:ASP187 3.0 42.6 1.0
CA A:ASP187 3.1 31.1 1.0
CB A:ASP187 3.2 28.3 1.0
O A:ASP187 3.3 42.4 1.0
N A:ARG188 3.5 38.4 1.0
C27 A:7YY403 3.6 57.9 1.0
C34 A:7YY403 3.6 50.9 1.0
CD2 A:HIS41 3.7 55.9 1.0
CG A:HIS41 4.0 54.3 1.0
C26 A:7YY403 4.1 45.9 1.0
SD A:MET165 4.2 41.2 1.0
CB A:HIS41 4.2 45.9 1.0
CA A:ARG188 4.3 44.1 1.0
O A:ARG188 4.4 56.0 1.0
NE2 A:HIS41 4.4 64.0 1.0
N A:ASP187 4.5 39.5 1.0
CB A:MET165 4.5 35.0 1.0
C A:ARG188 4.5 47.2 1.0
OH A:TYR54 4.5 36.1 1.0
CG A:ASP187 4.6 34.0 1.0
F28 A:7YY403 4.7 66.8 1.0
ND1 A:HIS41 4.8 53.8 1.0
O A:HIS164 4.8 43.2 1.0
O A:VAL186 4.8 34.6 1.0
CG A:MET165 4.9 29.3 1.0

Fluorine binding site 3 out of 6 in 8dz0

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


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 Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:53.8
occ:1.00
 F33 A:7YY403 0.0 53.8 1.0
C32 A:7YY403 1.4 57.3 1.0
C34 A:7YY403 2.4 50.9 1.0
C30 A:7YY403 2.4 46.9 1.0
F31 A:7YY403 2.8 51.6 1.0
O A:HIS164 3.0 43.2 1.0
CG A:HIS41 3.0 54.3 1.0
CB A:HIS41 3.1 45.9 1.0
ND1 A:HIS41 3.3 53.8 1.0
C26 A:7YY403 3.6 45.9 1.0
C29 A:7YY403 3.7 54.0 1.0
CD2 A:HIS41 3.7 55.9 1.0
C A:HIS164 3.9 31.9 1.0
CE1 A:HIS41 4.0 64.8 1.0
C27 A:7YY403 4.1 57.9 1.0
NE2 A:HIS41 4.2 64.0 1.0
SG A:CYS145 4.2 50.5 1.0
CA A:HIS164 4.4 25.6 1.0
CB A:HIS164 4.4 22.3 1.0
CA A:HIS41 4.6 39.2 1.0
CB A:MET165 4.6 35.0 1.0
CL2 A:7YY403 4.7 66.0 1.0
N A:MET165 4.8 27.5 1.0
CB A:ASP187 4.9 28.3 1.0
N24 A:7YY403 4.9 43.9 1.0
C25 A:7YY403 4.9 47.6 1.0
CA A:MET165 5.0 28.0 1.0

Fluorine binding site 4 out of 6 in 8dz0

Go back to Fluorine Binding Sites List in 8dz0
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir


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 Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:88.5
occ:1.00
 F28 B:7YY402 0.0 88.5 1.0
C27 B:7YY402 1.4 74.8 1.0
C26 B:7YY402 2.4 74.7 1.0
C29 B:7YY402 2.4 72.5 1.0
C25 B:7YY402 2.8 72.9 1.0
C30 B:7YY402 3.6 72.1 1.0
C34 B:7YY402 3.6 83.0 1.0
C32 B:7YY402 4.1 81.1 1.0
N24 B:7YY402 4.2 69.7 1.0
O B:ARG188 4.4 63.0 1.0
CB B:MET165 4.5 47.8 1.0
O36 B:7YY402 4.5 68.8 1.0
CA B:GLN189 4.5 84.8 1.0
CB B:GLN189 4.5 93.9 1.0
C B:ARG188 4.6 73.9 1.0
N B:GLN189 4.7 83.5 1.0
OE1 B:GLN189 4.7 118.9 1.0
F31 B:7YY402 4.8 83.1 1.0
C35 B:7YY402 4.8 71.4 1.0

Fluorine binding site 5 out of 6 in 8dz0

Go back to Fluorine Binding Sites List in 8dz0
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir


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 Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:83.1
occ:1.00
 F31 B:7YY402 0.0 83.1 1.0
C30 B:7YY402 1.4 72.1 1.0
C32 B:7YY402 2.4 81.1 1.0
C29 B:7YY402 2.4 72.5 1.0
F33 B:7YY402 2.7 67.4 1.0
C B:ASP187 2.9 62.5 1.0
CA B:ASP187 3.0 51.2 1.0
CD2 B:HIS41 3.1 81.0 1.0
CB B:ASP187 3.2 45.3 1.0
O B:ASP187 3.2 64.2 1.0
N B:ARG188 3.3 67.9 1.0
C34 B:7YY402 3.6 83.0 1.0
C27 B:7YY402 3.6 74.8 1.0
CG B:HIS41 3.7 81.4 1.0
NE2 B:HIS41 3.8 79.3 1.0
SD B:MET165 3.9 43.2 1.0
CA B:ARG188 4.0 74.8 1.0
C26 B:7YY402 4.1 74.7 1.0
CB B:HIS41 4.1 66.9 1.0
O B:HIS164 4.5 49.8 1.0
N B:ASP187 4.5 49.4 1.0
CB B:MET165 4.5 47.8 1.0
CG B:ASP187 4.5 53.5 1.0
OH B:TYR54 4.6 64.6 1.0
C B:ARG188 4.6 73.9 1.0
O B:ARG188 4.6 63.0 1.0
ND1 B:HIS41 4.7 94.5 1.0
CE1 B:HIS41 4.7 89.5 1.0
F28 B:7YY402 4.8 88.5 1.0
O B:VAL186 4.8 52.5 1.0
CG B:MET165 4.8 41.1 1.0
OD2 B:ASP187 5.0 59.4 1.0

Fluorine binding site 6 out of 6 in 8dz0

Go back to Fluorine Binding Sites List in 8dz0
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir


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 Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:67.4
occ:1.00
 F33 B:7YY402 0.0 67.4 1.0
C32 B:7YY402 1.4 81.1 1.0
C34 B:7YY402 2.4 83.0 1.0
C30 B:7YY402 2.4 72.1 1.0
F31 B:7YY402 2.7 83.1 1.0
O B:HIS164 3.0 49.8 1.0
CB B:HIS41 3.1 66.9 1.0
CG B:HIS41 3.1 81.4 1.0
CD2 B:HIS41 3.5 81.0 1.0
C26 B:7YY402 3.6 74.7 1.0
C29 B:7YY402 3.7 72.5 1.0
ND1 B:HIS41 3.7 94.5 1.0
C B:HIS164 3.9 37.6 1.0
SG B:CYS145 4.1 62.5 1.0
C27 B:7YY402 4.1 74.8 1.0
NE2 B:HIS41 4.2 79.3 1.0
ND1 B:HIS164 4.2 50.0 1.0
CE1 B:HIS41 4.3 89.5 1.0
CA B:HIS164 4.4 32.0 1.0
CA B:HIS41 4.6 65.6 1.0
CB B:HIS164 4.6 37.0 1.0
CL2 B:7YY402 4.7 71.8 1.0
CB B:MET165 4.8 47.8 1.0
C25 B:7YY402 4.9 72.9 1.0
CG B:HIS164 4.9 43.7 1.0
N24 B:7YY402 4.9 69.7 1.0
CB B:ASP187 5.0 45.3 1.0
N B:MET165 5.0 41.7 1.0

Reference:

G.D.Noske, G.Oliva, A.S.Godoy. Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ensitrelvir To Be Published.
Page generated: Wed Jul 16 03:31:00 2025

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