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Fluorine in PDB 9cjr: X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir

Enzymatic activity of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir

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

Protein crystallography data

The structure of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir, PDB code: 9cjr was solved by M.A.Esler, K.Shi, R.S.Harris, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.62 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.437, 99.397, 57.077, 90, 105.76, 90
R / Rfree (%) 17.4 / 21.5

Other elements in 9cjr:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir (pdb code 9cjr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir, PDB code: 9cjr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9cjr

Go back to Fluorine Binding Sites List in 9cjr
Fluorine binding site 1 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:38.0
occ:1.00
 F28 A:7YY401 0.0 38.0 1.0
C27 A:7YY401 1.4 27.8 1.0
C29 A:7YY401 2.3 29.3 1.0
C26 A:7YY401 2.4 29.3 1.0
H16 A:7YY401 2.5 35.2 1.0
H15 A:7YY401 2.7 37.9 1.0
C25 A:7YY401 2.8 31.5 1.0
H14 A:7YY401 2.9 37.9 1.0
CA A:GLN189 3.0 38.1 1.0
O A:HOH527 3.2 31.1 1.0
CB A:GLN189 3.2 42.9 1.0
CG A:GLN189 3.3 56.3 1.0
O A:HOH586 3.5 36.0 1.0
C30 A:7YY401 3.6 31.5 1.0
O A:HOH552 3.6 31.9 1.0
C34 A:7YY401 3.6 23.5 1.0
N A:GLN189 3.7 39.8 1.0
O A:ARG188 3.8 36.9 1.0
NE2 A:GLN189 3.8 67.0 1.0
CD A:GLN189 3.9 55.6 1.0
O A:HOH614 3.9 44.0 1.0
C A:ARG188 4.0 40.3 1.0
C32 A:7YY401 4.1 28.3 1.0
C A:GLN189 4.2 50.6 1.0
N24 A:7YY401 4.3 28.9 1.0
H17 A:7YY401 4.4 28.2 1.0
CB A:MET165 4.4 32.6 1.0
H8 A:7YY401 4.5 33.0 1.0
NE2 A:HIS41 4.6 36.3 1.0
O36 A:7YY401 4.7 29.6 1.0
N A:THR190 4.7 48.5 1.0
F31 A:7YY401 4.7 46.9 1.0
OE1 A:GLN189 4.8 55.4 1.0
SD A:MET165 4.9 38.9 1.0
C35 A:7YY401 4.9 33.5 1.0
CE1 A:HIS41 5.0 39.8 1.0

Fluorine binding site 2 out of 6 in 9cjr

Go back to Fluorine Binding Sites List in 9cjr
Fluorine binding site 2 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:46.9
occ:1.00
 F31 A:7YY401 0.0 46.9 1.0
C30 A:7YY401 1.3 31.5 1.0
C32 A:7YY401 2.3 28.3 1.0
C29 A:7YY401 2.4 29.3 1.0
H16 A:7YY401 2.6 35.2 1.0
F33 A:7YY401 2.7 30.3 1.0
CB A:ASP187 3.0 34.2 1.0
CA A:ASP187 3.1 33.0 1.0
C A:ASP187 3.2 42.0 1.0
ND1 A:HIS41 3.4 33.8 1.0
C27 A:7YY401 3.6 27.8 1.0
C34 A:7YY401 3.6 23.5 1.0
O A:ASP187 3.6 40.0 1.0
CG A:HIS41 3.6 31.2 1.0
CE1 A:HIS41 3.8 39.8 1.0
N A:ARG188 3.8 41.9 1.0
CD2 A:HIS41 4.1 35.6 1.0
CB A:HIS41 4.1 27.2 1.0
C26 A:7YY401 4.1 29.3 1.0
SD A:MET165 4.1 38.9 1.0
NE2 A:HIS41 4.1 36.3 1.0
H17 A:7YY401 4.4 28.2 1.0
CG A:ASP187 4.4 44.7 1.0
N A:ASP187 4.5 33.8 1.0
OH A:TYR54 4.5 41.3 1.0
CA A:ARG188 4.6 43.7 1.0
CD2 A:HIS164 4.6 18.4 1.0
C A:ARG188 4.6 40.3 1.0
O A:ARG188 4.7 36.9 1.0
CB A:MET165 4.7 32.6 1.0
CB A:HIS164 4.7 24.5 1.0
F28 A:7YY401 4.7 38.0 1.0
CG A:MET165 4.9 35.9 1.0
O A:VAL186 4.9 29.8 1.0
OD2 A:ASP187 4.9 30.1 1.0

Fluorine binding site 3 out of 6 in 9cjr

Go back to Fluorine Binding Sites List in 9cjr
Fluorine binding site 3 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.3
occ:1.00
 F33 A:7YY401 0.0 30.3 1.0
C32 A:7YY401 1.4 28.3 1.0
C30 A:7YY401 2.3 31.5 1.0
C34 A:7YY401 2.4 23.5 1.0
H17 A:7YY401 2.6 28.2 1.0
F31 A:7YY401 2.7 46.9 1.0
O A:HIS164 3.2 29.6 1.0
CB A:HIS41 3.4 27.2 1.0
CG A:HIS41 3.4 31.2 1.0
SG A:CYS145 3.5 28.1 1.0
CD2 A:HIS41 3.5 35.6 1.0
C29 A:7YY401 3.6 29.3 1.0
C26 A:7YY401 3.6 29.3 1.0
C A:HIS164 3.8 24.2 1.0
CB A:HIS164 3.9 24.5 1.0
CA A:HIS164 4.0 19.4 1.0
C27 A:7YY401 4.1 27.8 1.0
CD2 A:HIS164 4.1 18.4 1.0
ND1 A:HIS41 4.2 33.8 1.0
CL2 A:7YY401 4.3 29.7 1.0
CG A:HIS164 4.3 19.6 1.0
NE2 A:HIS41 4.3 36.3 1.0
H16 A:7YY401 4.4 35.2 1.0
CE1 A:HIS41 4.7 39.8 1.0
N A:MET165 4.7 23.7 1.0
CB A:MET165 4.7 32.6 1.0
CB A:PRO39 4.8 16.4 1.0
CA A:HIS41 4.9 28.0 1.0
C25 A:7YY401 4.9 31.5 1.0
N24 A:7YY401 4.9 28.9 1.0
CB A:ASP187 5.0 34.2 1.0
CB A:CYS145 5.0 20.6 1.0

Fluorine binding site 4 out of 6 in 9cjr

Go back to Fluorine Binding Sites List in 9cjr
Fluorine binding site 4 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:35.4
occ:1.00
 F28 B:7YY401 0.0 35.4 1.0
C27 B:7YY401 1.4 33.2 1.0
C29 B:7YY401 2.3 23.3 1.0
C26 B:7YY401 2.4 27.1 1.0
H16 B:7YY401 2.5 28.0 1.0
H15 B:7YY401 2.7 32.0 1.0
C25 B:7YY401 2.8 26.7 1.0
H14 B:7YY401 2.9 32.0 1.0
O B:HOH588 3.1 33.8 1.0
CA B:GLN189 3.1 44.5 1.0
O B:HOH517 3.4 35.2 1.0
CB B:GLN189 3.4 39.5 1.0
CG B:GLN189 3.5 37.1 1.0
O B:ARG188 3.5 35.4 1.0
C30 B:7YY401 3.6 34.3 1.0
C34 B:7YY401 3.6 25.8 1.0
O B:HOH564 3.7 33.1 1.0
N B:GLN189 3.7 42.6 1.0
C B:ARG188 3.9 41.3 1.0
NE2 B:GLN189 4.1 47.6 1.0
C32 B:7YY401 4.1 31.1 1.0
CD B:GLN189 4.1 41.1 1.0
N24 B:7YY401 4.3 23.1 1.0
C B:GLN189 4.3 36.8 1.0
CB B:MET165 4.4 35.8 1.0
H17 B:7YY401 4.4 31.0 1.0
H8 B:7YY401 4.5 33.3 1.0
N B:THR190 4.6 34.8 1.0
O36 B:7YY401 4.7 25.2 1.0
NE2 B:HIS41 4.7 29.8 1.0
F31 B:7YY401 4.7 37.3 1.0
SD B:MET165 4.8 38.0 1.0
C35 B:7YY401 5.0 24.5 1.0

Fluorine binding site 5 out of 6 in 9cjr

Go back to Fluorine Binding Sites List in 9cjr
Fluorine binding site 5 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:37.3
occ:1.00
 F31 B:7YY401 0.0 37.3 1.0
C30 B:7YY401 1.3 34.3 1.0
C32 B:7YY401 2.3 31.1 1.0
C29 B:7YY401 2.4 23.3 1.0
H16 B:7YY401 2.6 28.0 1.0
F33 B:7YY401 2.7 24.5 1.0
CB B:ASP187 2.9 30.3 1.0
CA B:ASP187 2.9 29.2 1.0
C B:ASP187 3.2 30.5 1.0
ND1 B:HIS41 3.6 28.2 1.0
C27 B:7YY401 3.6 33.2 1.0
C34 B:7YY401 3.6 25.8 1.0
O B:ASP187 3.7 33.0 1.0
CG B:HIS41 3.7 33.3 1.0
N B:ARG188 3.8 39.2 1.0
CE1 B:HIS41 4.0 40.4 1.0
CB B:HIS41 4.0 22.9 1.0
O B:HOH584 4.1 25.2 1.0
C26 B:7YY401 4.1 27.1 1.0
CD2 B:HIS41 4.2 25.9 1.0
SD B:MET165 4.2 38.0 1.0
CG B:ASP187 4.3 30.8 1.0
OH B:TYR54 4.3 27.2 1.0
N B:ASP187 4.3 28.8 1.0
NE2 B:HIS41 4.3 29.8 1.0
H17 B:7YY401 4.4 31.0 1.0
ND1 B:HIS164 4.5 27.1 1.0
CA B:ARG188 4.7 40.3 1.0
O B:ARG188 4.7 35.4 1.0
F28 B:7YY401 4.7 35.4 1.0
O B:VAL186 4.7 30.7 1.0
CB B:HIS164 4.7 21.7 1.0
C B:ARG188 4.7 41.3 1.0
CB B:MET165 4.8 35.8 1.0
OD2 B:ASP187 4.8 33.9 1.0
C B:VAL186 5.0 35.9 1.0

Fluorine binding site 6 out of 6 in 9cjr

Go back to Fluorine Binding Sites List in 9cjr
Fluorine binding site 6 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:24.5
occ:1.00
 F33 B:7YY401 0.0 24.5 1.0
C32 B:7YY401 1.4 31.1 1.0
C30 B:7YY401 2.3 34.3 1.0
C34 B:7YY401 2.4 25.8 1.0
H17 B:7YY401 2.6 31.0 1.0
F31 B:7YY401 2.7 37.3 1.0
O B:HIS164 3.2 25.8 1.0
CB B:HIS41 3.3 22.9 1.0
SG B:CYS145 3.4 26.2 1.0
CG B:HIS41 3.5 33.3 1.0
C29 B:7YY401 3.6 23.3 1.0
C26 B:7YY401 3.6 27.1 1.0
CD2 B:HIS41 3.7 25.9 1.0
C B:HIS164 3.8 17.5 1.0
ND1 B:HIS164 3.9 27.1 1.0
CB B:HIS164 4.0 21.7 1.0
CA B:HIS164 4.0 21.0 1.0
C27 B:7YY401 4.1 33.2 1.0
O B:HOH584 4.2 25.2 1.0
ND1 B:HIS41 4.3 28.2 1.0
CL2 B:7YY401 4.3 29.4 1.0
CG B:HIS164 4.4 21.9 1.0
H16 B:7YY401 4.4 28.0 1.0
NE2 B:HIS41 4.6 29.8 1.0
CB B:PRO39 4.8 16.3 1.0
CA B:HIS41 4.8 25.5 1.0
N B:MET165 4.8 20.4 1.0
CB B:MET165 4.9 35.8 1.0
CE1 B:HIS41 4.9 40.4 1.0
C25 B:7YY401 4.9 26.7 1.0
CB B:CYS145 4.9 22.6 1.0
CB B:ASP187 4.9 30.3 1.0
N24 B:7YY401 4.9 23.1 1.0

Reference:

M.A.Esler, K.Shi, R.S.Harris, H.Aihara. X-Ray Crystal Structure of Sars-Cov-2 Main Protease Double Mutants in Complex with Ensitrelvir To Be Published.
Page generated: Wed Jul 16 10:43:07 2025

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