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Fluorine in PDB 8wz0: Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor

Enzymatic activity of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor

All present enzymatic activity of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor:
3.4.22.69;

Protein crystallography data

The structure of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor, PDB code: 8wz0 was solved by J.Peng, D.Sun, X.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.91 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.54, 52.94, 113.96, 90, 100.72, 90
R / Rfree (%) 25.1 / 29.9

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor (pdb code 8wz0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor, PDB code: 8wz0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 8wz0

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Fluorine binding site 1 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:32.7
occ:1.00
 F22 A:XQF401 0.0 32.7 1.0
C20 A:XQF401 1.4 33.0 1.0
C19 A:XQF401 2.4 34.0 1.0
SG A:CYS145 2.6 33.5 1.0
O24 A:XQF401 2.7 34.9 1.0
CB A:CYS145 2.9 31.8 1.0
N A:CYS145 3.2 30.6 1.0
CA A:GLY143 3.3 29.7 1.0
N A:GLY143 3.3 29.7 1.0
C A:GLY143 3.6 29.6 1.0
N8 A:XQF401 3.6 35.7 1.0
CA A:CYS145 3.6 31.3 1.0
N A:SER144 3.7 29.3 1.0
NE2 A:HIS41 4.0 32.6 1.0
C6 A:XQF401 4.1 34.5 1.0
CB A:LEU27 4.2 34.0 1.0
O A:GLY143 4.3 30.5 1.0
C A:SER144 4.4 29.3 1.0
C7 A:XQF401 4.4 32.9 1.0
O A:CYS145 4.5 32.1 1.0
C A:ASN142 4.6 31.4 1.0
CD2 A:LEU27 4.6 33.9 1.0
C A:CYS145 4.6 32.2 1.0
CA A:SER144 4.7 29.4 1.0
C5 A:XQF401 4.8 34.6 1.0
CE1 A:HIS41 4.8 31.7 1.0
C9 A:XQF401 4.8 36.9 1.0
OG A:SER144 5.0 28.6 1.0

Fluorine binding site 2 out of 12 in 8wz0

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Fluorine binding site 2 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:43.5
occ:1.00
 F31 A:XQF401 0.0 43.5 1.0
C28 A:XQF401 1.4 43.2 1.0
F32 A:XQF401 2.3 44.3 1.0
C27 A:XQF401 2.4 42.7 1.0
C29 A:XQF401 2.4 42.2 1.0
O A:THR190 3.4 43.0 1.0
C30 A:XQF401 3.7 41.8 1.0
C26 A:XQF401 3.7 42.6 1.0
CD A:PRO168 3.9 45.2 1.0
C A:THR190 4.0 41.6 1.0
C12 A:XQF401 4.1 41.8 1.0
CG A:PRO168 4.2 45.9 1.0
O A:GLU166 4.2 37.3 1.0
N A:THR190 4.3 39.5 1.0
N A:ALA191 4.5 42.3 1.0
CA A:ALA191 4.7 43.2 1.0
CA A:GLN189 4.7 36.5 1.0
CA A:THR190 4.7 41.1 1.0
C A:GLN189 4.8 37.0 1.0
CG A:GLN189 4.8 36.0 1.0
N A:PRO168 4.9 45.0 1.0

Fluorine binding site 3 out of 12 in 8wz0

Go back to Fluorine Binding Sites List in 8wz0
Fluorine binding site 3 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.3
occ:1.00
 F32 A:XQF401 0.0 44.3 1.0
C28 A:XQF401 1.4 43.2 1.0
F31 A:XQF401 2.3 43.5 1.0
C27 A:XQF401 2.4 42.7 1.0
C29 A:XQF401 2.4 42.2 1.0
C30 A:XQF401 2.9 41.8 1.0
C26 A:XQF401 2.9 42.6 1.0
CG A:GLN189 3.4 36.0 1.0
C12 A:XQF401 3.5 41.8 1.0
CD A:GLN189 4.1 36.1 1.0
CB A:GLN189 4.3 35.4 1.0
CA A:GLN189 4.4 36.5 1.0
OE1 A:GLN189 4.5 37.7 1.0
N11 A:XQF401 4.6 40.9 1.0
NE2 A:GLN189 4.7 35.6 1.0
C A:GLN189 4.8 37.0 1.0
N A:THR190 4.9 39.5 1.0

Fluorine binding site 4 out of 12 in 8wz0

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Fluorine binding site 4 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.6
occ:1.00
 F34 A:XQF401 0.0 35.6 1.0
C1 A:XQF401 1.4 34.5 1.0
F35 A:XQF401 2.2 34.7 1.0
F36 A:XQF401 2.3 35.5 1.0
O33 A:XQF401 2.3 34.1 1.0
CG A:MET49 3.4 43.6 1.0
O A:ASP187 3.5 31.6 1.0
OH A:TYR54 3.6 28.0 1.0
C3 A:XQF401 3.6 34.1 1.0
CA A:MET49 3.6 42.8 1.0
CB A:MET49 3.7 42.4 1.0
O A:MET49 3.8 40.4 1.0
CB A:HIS41 3.9 29.9 1.0
C A:ASP187 4.0 33.9 1.0
CA A:ARG188 4.0 38.3 1.0
C A:MET49 4.2 40.9 1.0
N A:ARG188 4.2 34.8 1.0
N A:GLN189 4.3 35.2 1.0
C4 A:XQF401 4.4 34.9 1.0
C A:ARG188 4.4 36.1 1.0
SG A:CYS44 4.5 37.3 1.0
C2 A:XQF401 4.6 33.1 1.0
CG A:HIS41 4.6 30.7 1.0
CG A:PRO52 4.7 31.2 1.0
SD A:MET49 4.8 44.6 1.0
N A:MET49 4.8 43.3 1.0
CZ A:TYR54 4.9 27.9 1.0
CB A:CYS44 4.9 36.0 1.0
CE A:MET49 4.9 44.4 1.0
CA A:HIS41 5.0 30.0 1.0

Fluorine binding site 5 out of 12 in 8wz0

Go back to Fluorine Binding Sites List in 8wz0
Fluorine binding site 5 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.7
occ:1.00
 F35 A:XQF401 0.0 34.7 1.0
C1 A:XQF401 1.4 34.5 1.0
F34 A:XQF401 2.2 35.6 1.0
F36 A:XQF401 2.2 35.5 1.0
O33 A:XQF401 2.3 34.1 1.0
C3 A:XQF401 3.0 34.1 1.0
C4 A:XQF401 3.0 34.9 1.0
C A:ASP187 3.2 33.9 1.0
O A:ASP187 3.3 31.6 1.0
N A:ARG188 3.5 34.8 1.0
CE A:MET165 3.5 51.4 1.0
CA A:ASP187 3.6 33.0 1.0
CB A:HIS41 3.7 29.9 1.0
CB A:ASP187 3.9 31.8 1.0
CG A:HIS41 3.9 30.7 1.0
CA A:ARG188 4.0 38.3 1.0
ND1 A:HIS41 4.1 30.6 1.0
OH A:TYR54 4.1 28.0 1.0
C A:ARG188 4.3 36.1 1.0
C5 A:XQF401 4.4 34.6 1.0
C2 A:XQF401 4.4 33.1 1.0
O A:ARG188 4.7 34.7 1.0
CD2 A:HIS41 4.7 32.0 1.0
O A:HIS164 4.8 34.3 1.0
O A:HOH505 4.8 17.0 1.0
N A:GLN189 4.8 35.2 1.0
CE1 A:HIS41 4.9 31.7 1.0

Fluorine binding site 6 out of 12 in 8wz0

Go back to Fluorine Binding Sites List in 8wz0
Fluorine binding site 6 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.5
occ:1.00
 F36 A:XQF401 0.0 35.5 1.0
C1 A:XQF401 1.4 34.5 1.0
F35 A:XQF401 2.2 34.7 1.0
F34 A:XQF401 2.3 35.6 1.0
O33 A:XQF401 2.3 34.1 1.0
C3 A:XQF401 2.9 34.1 1.0
C4 A:XQF401 3.4 34.9 1.0
N A:GLN189 3.4 35.2 1.0
C A:ARG188 3.6 36.1 1.0
C2 A:XQF401 3.8 33.1 1.0
CA A:GLN189 3.9 36.5 1.0
CB A:GLN189 4.0 35.4 1.0
CA A:ARG188 4.0 38.3 1.0
O A:ARG188 4.1 34.7 1.0
CG A:MET49 4.1 43.6 1.0
CB A:MET49 4.1 42.4 1.0
N A:ARG188 4.2 34.8 1.0
O A:MET49 4.2 40.4 1.0
CE A:MET165 4.2 51.4 1.0
CE A:MET49 4.2 44.4 1.0
C30 A:XQF401 4.4 41.8 1.0
C A:ASP187 4.5 33.9 1.0
C5 A:XQF401 4.5 34.6 1.0
CA A:MET49 4.6 42.8 1.0
O A:ASP187 4.6 31.6 1.0
C29 A:XQF401 4.6 42.2 1.0
C A:MET49 4.8 40.9 1.0
C7 A:XQF401 4.8 32.9 1.0
SD A:MET49 4.9 44.6 1.0

Fluorine binding site 7 out of 12 in 8wz0

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Fluorine binding site 7 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:30.7
occ:1.00
 F22 B:XQF401 0.0 30.7 1.0
C20 B:XQF401 1.4 32.0 1.0
C19 B:XQF401 2.4 33.4 1.0
SG B:CYS145 2.6 30.5 1.0
O24 B:XQF401 2.6 33.9 1.0
CB B:CYS145 2.9 29.2 1.0
N B:CYS145 3.1 28.4 1.0
CA B:GLY143 3.2 29.0 1.0
N B:GLY143 3.2 30.2 1.0
C B:GLY143 3.4 28.7 1.0
N B:SER144 3.5 28.6 1.0
CA B:CYS145 3.6 28.5 1.0
N8 B:XQF401 3.6 35.6 1.0
O B:GLY143 4.0 29.9 1.0
C6 B:XQF401 4.2 34.9 1.0
C B:SER144 4.2 28.3 1.0
CB B:LEU27 4.2 35.6 1.0
NE2 B:HIS41 4.2 31.1 1.0
CA B:SER144 4.4 28.6 1.0
O B:CYS145 4.4 27.6 1.0
C B:ASN142 4.5 32.8 1.0
C7 B:XQF401 4.5 34.1 1.0
C B:CYS145 4.5 28.1 1.0
CD2 B:LEU27 4.7 34.4 1.0
OG B:SER144 4.8 28.6 1.0
C9 B:XQF401 4.8 37.1 1.0
C5 B:XQF401 4.9 35.2 1.0
CE1 B:HIS41 4.9 30.9 1.0

Fluorine binding site 8 out of 12 in 8wz0

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Fluorine binding site 8 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.1
occ:1.00
 F31 B:XQF401 0.0 40.1 1.0
C28 B:XQF401 1.4 40.2 1.0
F32 B:XQF401 2.3 40.9 1.0
C27 B:XQF401 2.4 38.7 1.0
C29 B:XQF401 2.4 40.3 1.0
C30 B:XQF401 3.7 39.0 1.0
C26 B:XQF401 3.7 38.3 1.0
CD B:PRO168 4.0 47.6 1.0
O B:THR190 4.0 48.6 1.0
C12 B:XQF401 4.2 38.8 1.0
CG B:PRO168 4.2 48.0 1.0
O B:GLU166 4.4 38.9 1.0
N B:THR190 4.4 42.4 1.0
CG B:GLN189 4.5 36.3 1.0
C B:THR190 4.5 47.4 1.0
CA B:GLN189 4.6 37.0 1.0
C B:GLN189 4.7 38.8 1.0
SD B:MET165 4.8 40.1 0.5
N B:PRO168 4.9 47.2 1.0

Fluorine binding site 9 out of 12 in 8wz0

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Fluorine binding site 9 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.9
occ:1.00
 F32 B:XQF401 0.0 40.9 1.0
C28 B:XQF401 1.4 40.2 1.0
F31 B:XQF401 2.3 40.1 1.0
C27 B:XQF401 2.4 38.7 1.0
C29 B:XQF401 2.4 40.3 1.0
C30 B:XQF401 2.9 39.0 1.0
C26 B:XQF401 2.9 38.3 1.0
CG B:GLN189 3.4 36.3 1.0
C12 B:XQF401 3.5 38.8 1.0
CD B:GLN189 3.9 35.9 1.0
NE2 B:GLN189 4.1 37.1 1.0
CB B:GLN189 4.4 36.6 1.0
N11 B:XQF401 4.5 39.5 1.0
CA B:GLN189 4.6 37.0 1.0
OE1 B:GLN189 4.7 35.8 1.0

Fluorine binding site 10 out of 12 in 8wz0

Go back to Fluorine Binding Sites List in 8wz0
Fluorine binding site 10 out of 12 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:42.6
occ:1.00
 F34 B:XQF401 0.0 42.6 1.0
C1 B:XQF401 1.4 41.1 1.0
F35 B:XQF401 2.3 41.5 1.0
F36 B:XQF401 2.3 44.0 1.0
O33 B:XQF401 2.3 38.8 1.0
O B:ASP187 3.4 30.7 1.0
OH B:TYR54 3.5 35.5 1.0
C3 B:XQF401 3.6 36.4 1.0
CG B:MET49 3.7 42.7 1.0
CB B:HIS41 3.8 31.0 1.0
CA B:MET49 3.9 41.7 1.0
O B:MET49 3.9 42.0 1.0
CB B:MET49 3.9 41.4 1.0
C B:ASP187 3.9 32.3 1.0
CA B:ARG188 4.0 34.6 0.5
CA B:ARG188 4.0 34.4 0.5
N B:ARG188 4.1 32.9 0.5
N B:ARG188 4.2 33.0 0.5
C4 B:XQF401 4.4 35.2 1.0
N B:GLN189 4.4 35.7 1.0
C B:ARG188 4.4 34.6 0.5
C B:MET49 4.4 41.7 1.0
C B:ARG188 4.4 34.5 0.5
CG B:HIS41 4.5 31.2 1.0
C2 B:XQF401 4.6 34.6 1.0
SG B:CYS44 4.7 39.2 1.0
CG B:PRO52 4.7 40.2 1.0
CZ B:TYR54 4.8 36.0 1.0
CA B:ASP187 4.9 32.6 1.0
CE B:MET49 4.9 44.9 1.0
CA B:HIS41 5.0 30.6 1.0

Reference:

J.Peng, D.Sun, X.Ding. Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor To Be Published.
Page generated: Wed Jul 16 10:07:14 2025

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