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Fluorine in PDB 8v8e: Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)

Enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)

All present enzymatic activity of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv):
3.4.22.69;

Protein crystallography data

The structure of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv), PDB code: 8v8e was solved by A.Kovalevsky, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.83 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.476, 62.641, 58.583, 90, 100.23, 90
R / Rfree (%) 14.9 / 19.3

Other elements in 8v8e:

The structure of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) (pdb code 8v8e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv), PDB code: 8v8e:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8v8e

Go back to Fluorine Binding Sites List in 8v8e
Fluorine binding site 1 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:26.1
occ:0.98
 F28 A:7YY301 0.0 26.1 1.0
C27 A:7YY301 1.4 24.1 1.0
C29 A:7YY301 2.4 23.6 1.0
C26 A:7YY301 2.4 17.7 1.0
C25 A:7YY301 2.8 17.7 1.0
CA A:GLN189 3.3 39.1 1.0
CG A:GLN189 3.5 37.5 1.0
CB A:GLN189 3.5 33.0 1.0
C30 A:7YY301 3.6 25.5 1.0
C34 A:7YY301 3.6 22.5 1.0
O A:HOH425 3.8 21.2 1.0
O A:ARG188 3.9 28.6 1.0
N A:GLN189 4.0 30.2 1.0
C32 A:7YY301 4.1 20.8 1.0
OE1 A:GLN189 4.1 47.8 1.0
C A:ARG188 4.1 29.6 1.0
N24 A:7YY301 4.2 18.7 1.0
CD A:GLN189 4.2 51.9 1.0
CE A:MET165 4.3 32.6 1.0
CB A:MET165 4.5 18.2 1.0
C A:GLN189 4.5 44.5 1.0
O36 A:7YY301 4.5 19.3 1.0
NE2 A:HIS41 4.7 21.1 1.0
F31 A:7YY301 4.7 24.3 1.0
C35 A:7YY301 4.9 17.6 1.0
N A:THR190 5.0 46.2 1.0

Fluorine binding site 2 out of 6 in 8v8e

Go back to Fluorine Binding Sites List in 8v8e
Fluorine binding site 2 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:24.3
occ:0.98
 F31 A:7YY301 0.0 24.3 1.0
C30 A:7YY301 1.3 25.5 1.0
C32 A:7YY301 2.4 20.8 1.0
C29 A:7YY301 2.4 23.6 1.0
F33 A:7YY301 2.7 18.8 1.0
CB A:ASP187 3.1 15.8 1.0
CA A:ASP187 3.1 24.2 1.0
C A:ASP187 3.2 20.5 1.0
CE A:MET165 3.2 32.6 1.0
ND1 A:HIS41 3.4 18.1 1.0
O A:ASP187 3.6 21.8 1.0
N A:ARG188 3.6 23.4 1.0
C27 A:7YY301 3.6 24.1 1.0
C34 A:7YY301 3.6 22.5 1.0
CG A:HIS41 3.7 21.2 1.0
CE1 A:HIS41 3.9 20.2 1.0
CB A:HIS41 4.1 17.3 1.0
C26 A:7YY301 4.1 17.7 1.0
CD2 A:HIS41 4.2 15.0 1.0
O A:HOH429 4.2 18.0 1.0
NE2 A:HIS41 4.3 21.1 1.0
CA A:ARG188 4.4 30.3 1.0
CG A:ASP187 4.4 19.4 1.0
OH A:TYR54 4.5 18.9 1.0
N A:ASP187 4.6 20.6 1.0
CD2 A:HIS164 4.6 14.2 1.0
CB A:HIS164 4.6 11.4 1.0
C A:ARG188 4.6 29.6 1.0
O A:ARG188 4.7 28.6 1.0
F28 A:7YY301 4.7 26.1 1.0
SD A:MET165 4.8 42.0 1.0
CB A:MET165 4.9 18.2 1.0
OD2 A:ASP187 4.9 15.9 1.0
O A:VAL186 4.9 21.2 1.0

Fluorine binding site 3 out of 6 in 8v8e

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Fluorine binding site 3 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:18.8
occ:0.98
 F33 A:7YY301 0.0 18.8 1.0
C32 A:7YY301 1.3 20.8 1.0
C30 A:7YY301 2.4 25.5 1.0
C34 A:7YY301 2.4 22.5 1.0
F31 A:7YY301 2.7 24.3 1.0
CB A:HIS41 3.3 17.3 1.0
CG A:HIS41 3.4 21.2 1.0
O A:HIS164 3.4 14.5 1.0
SG A:CYS145 3.4 14.1 1.0
CD2 A:HIS41 3.6 15.0 1.0
C29 A:7YY301 3.6 23.6 1.0
C26 A:7YY301 3.6 17.7 1.0
CB A:HIS164 3.9 11.4 1.0
C A:HIS164 4.0 16.1 1.0
C27 A:7YY301 4.1 24.1 1.0
CA A:HIS164 4.1 12.4 1.0
CD2 A:HIS164 4.1 14.2 1.0
ND1 A:HIS41 4.1 18.1 1.0
O A:HOH429 4.2 18.0 1.0
CL2 A:7YY301 4.3 16.3 1.0
CG A:HIS164 4.3 16.8 1.0
NE2 A:HIS41 4.4 21.1 1.0
CB A:PRO39 4.7 11.9 1.0
CE1 A:HIS41 4.7 20.2 1.0
CA A:HIS41 4.8 17.6 1.0
C25 A:7YY301 4.9 17.7 1.0
CB A:CYS145 5.0 9.6 1.0
CE A:MET165 5.0 32.6 1.0
N A:MET165 5.0 12.0 1.0

Fluorine binding site 4 out of 6 in 8v8e

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Fluorine binding site 4 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:35.2
occ:0.75
 F28 B:7YY301 0.0 35.2 0.8
C27 B:7YY301 1.4 30.4 0.8
C29 B:7YY301 2.4 31.7 0.8
C26 B:7YY301 2.4 27.6 0.8
C25 B:7YY301 2.8 26.5 0.8
CG B:GLN189 3.3 46.3 1.0
C30 B:7YY301 3.6 35.4 0.8
C34 B:7YY301 3.6 22.5 0.8
O B:HOH435 3.6 31.9 1.0
NE2 B:GLN189 3.8 55.3 1.0
O B:ARG188 4.0 35.6 1.0
CD B:GLN189 4.1 58.4 1.0
C32 B:7YY301 4.1 31.0 0.8
O B:HOH466 4.2 43.3 1.0
N24 B:7YY301 4.2 22.4 0.8
CB B:MET165 4.2 26.9 1.0
C B:ARG188 4.4 47.2 1.0
CB B:GLN189 4.4 50.5 1.0
O36 B:7YY301 4.5 24.7 0.8
NE2 B:HIS41 4.6 38.0 1.0
N B:GLN189 4.6 41.1 1.0
CA B:GLN189 4.6 52.8 1.0
SD B:MET165 4.7 37.2 1.0
F31 B:7YY301 4.7 35.6 0.8
C35 B:7YY301 4.8 24.0 0.8

Fluorine binding site 5 out of 6 in 8v8e

Go back to Fluorine Binding Sites List in 8v8e
Fluorine binding site 5 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:35.6
occ:0.75
 F31 B:7YY301 0.0 35.6 0.8
C30 B:7YY301 1.3 35.4 0.8
C32 B:7YY301 2.4 31.0 0.8
C29 B:7YY301 2.4 31.7 0.8
F33 B:7YY301 2.7 28.8 0.8
CB B:ASP187 3.0 15.9 1.0
CA B:ASP187 3.1 16.7 1.0
C B:ASP187 3.2 27.1 1.0
C27 B:7YY301 3.6 30.4 0.8
N B:ARG188 3.6 34.6 1.0
C34 B:7YY301 3.6 22.5 0.8
CG B:HIS41 3.6 28.0 1.0
ND1 B:HIS41 3.6 29.0 1.0
O B:ASP187 3.7 23.3 1.0
SD B:MET165 3.8 37.2 1.0
CE1 B:HIS41 4.0 35.2 1.0
CD2 B:HIS41 4.0 36.0 1.0
CB B:HIS41 4.0 21.8 1.0
O B:HOH449 4.1 17.2 1.0
C26 B:7YY301 4.1 27.6 0.8
NE2 B:HIS41 4.2 38.0 1.0
CG B:ASP187 4.3 16.7 1.0
CA B:ARG188 4.4 40.0 1.0
CB B:MET165 4.4 26.9 1.0
N B:ASP187 4.6 18.1 1.0
OH B:TYR54 4.6 19.6 1.0
CB B:HIS164 4.7 16.9 1.0
O B:ARG188 4.7 35.6 1.0
F28 B:7YY301 4.7 35.2 0.8
ND1 B:HIS164 4.8 12.9 1.0
CG B:MET165 4.8 25.6 1.0
OD2 B:ASP187 4.8 18.1 1.0
O B:HIS164 4.9 20.6 1.0
C B:ARG188 4.9 47.2 1.0

Fluorine binding site 6 out of 6 in 8v8e

Go back to Fluorine Binding Sites List in 8v8e
Fluorine binding site 6 out of 6 in the Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Room-Temperature X-Ray Structure of Sars-Cov-2 Main Protease Catalytic Domain (Residues 1-199-6H) in Complex with Ensitrelvir (Esv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:28.8
occ:0.75
 F33 B:7YY301 0.0 28.8 0.8
C32 B:7YY301 1.4 31.0 0.8
C30 B:7YY301 2.4 35.4 0.8
C34 B:7YY301 2.4 22.5 0.8
F31 B:7YY301 2.7 35.6 0.8
CB B:HIS41 3.1 21.8 1.0
O B:HIS164 3.1 20.6 1.0
CG B:HIS41 3.3 28.0 1.0
CD2 B:HIS41 3.5 36.0 1.0
C29 B:7YY301 3.6 31.7 0.8
C26 B:7YY301 3.7 27.6 0.8
SG B:CYS145 3.7 23.0 1.0
C B:HIS164 3.8 18.6 1.0
O B:HOH449 4.0 17.2 1.0
CB B:HIS164 4.0 16.9 1.0
CA B:HIS164 4.1 15.5 1.0
C27 B:7YY301 4.1 30.4 0.8
ND1 B:HIS164 4.2 12.9 1.0
ND1 B:HIS41 4.3 29.0 1.0
CL2 B:7YY301 4.4 23.8 0.8
CB B:PRO39 4.4 11.1 1.0
NE2 B:HIS41 4.4 38.0 1.0
CG B:HIS164 4.5 14.8 1.0
CB B:MET165 4.6 26.9 1.0
CA B:HIS41 4.6 20.3 1.0
CE1 B:HIS41 4.8 35.2 1.0
N B:MET165 4.8 14.2 1.0
C25 B:7YY301 4.9 26.5 0.8
N B:HIS41 5.0 13.5 1.0

Reference:

A.Kovalevsky, A.Aniana, L.Coates, R.Ghirlando, N.T.Nashed, J.M.Louis. Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of Sars-Cov-2 Main Protease. J.Mol.Biol. 68616 2024.
ISSN: ESSN 1089-8638
PubMed: 38762033
DOI: 10.1016/J.JMB.2024.168616
Page generated: Wed Jul 16 09:40:53 2025

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