Fluorine in PDB 8e26: Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir, PDB code: 8e26 was solved by G.D.Noske, A.S.Godoy, G.Oliva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.31 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.841, 100.619, 103.356, 90, 90, 90
R / Rfree (%) 22.4 / 26.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir (pdb code 8e26). 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 N142S Mutant in Complex with Nirmatrelvir, PDB code: 8e26:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8e26

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Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir


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 N142S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:26.2
occ:1.00
 F1 A:4WI401 0.0 26.2 1.0
C22 A:4WI401 1.3 26.0 1.0
F3 A:4WI401 2.1 27.1 1.0
F2 A:4WI401 2.1 25.8 1.0
HE3 A:MET165 2.3 16.9 1.0
C21 A:4WI401 2.4 24.4 1.0
H16 A:4WI401 2.7 22.6 1.0
N4 A:4WI401 2.9 22.6 1.0
HA A:LEU167 3.0 20.4 1.0
HD23 A:LEU167 3.0 21.3 1.0
O A:GLU166 3.1 17.7 1.0
CE A:MET165 3.3 16.9 1.0
O4 A:4WI401 3.3 25.4 1.0
HB2 A:MET165 3.5 14.0 1.0
HE2 A:MET165 3.5 16.9 1.0
HE1 A:MET165 3.7 16.9 1.0
HG A:LEU167 3.7 21.2 1.0
C A:GLU166 3.8 17.7 1.0
CD2 A:LEU167 3.8 21.4 1.0
CA A:LEU167 3.8 20.4 1.0
HD3 A:PRO168 3.9 23.2 1.0
HG3 A:MET165 3.9 15.1 1.0
HD22 A:LEU167 4.0 21.3 1.0
N A:LEU167 4.1 18.9 1.0
CG A:LEU167 4.2 21.2 1.0
C14 A:4WI401 4.3 21.2 1.0
O A:HOH528 4.3 26.5 1.0
CB A:MET165 4.3 14.1 1.0
HE22 A:GLN192 4.3 14.8 1.0
CG A:MET165 4.4 14.8 1.0
HB2 A:GLN192 4.4 16.2 1.0
HG3 A:GLN192 4.4 15.5 1.0
SD A:MET165 4.5 16.9 1.0
NE2 A:GLN192 4.5 14.8 1.0
HD21 A:LEU167 4.6 21.3 1.0
CB A:LEU167 4.6 20.6 1.0
H A:GLU166 4.6 15.1 1.0
O3 A:4WI401 4.6 19.1 1.0
C13 A:4WI401 4.6 19.8 1.0
H15 A:4WI401 4.7 21.1 1.0
N A:GLU166 4.7 15.1 1.0
H29 A:4WI401 4.8 20.4 1.0
CD A:PRO168 4.8 23.4 1.0
HB3 A:MET165 4.8 14.0 1.0
CD A:GLN192 4.8 14.8 1.0
HE21 A:GLN192 4.8 14.8 1.0
H A:LEU167 4.9 18.9 1.0
HB3 A:LEU167 4.9 20.7 1.0
C A:LEU167 4.9 21.7 1.0
CA A:GLU166 4.9 16.8 1.0
CG A:GLN192 4.9 15.6 1.0
HD2 A:PRO168 4.9 23.2 1.0
H23 A:4WI401 5.0 17.4 1.0

Fluorine binding site 2 out of 6 in 8e26

Go back to Fluorine Binding Sites List in 8e26
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir


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 N142S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:25.8
occ:1.00
 F2 A:4WI401 0.0 25.8 1.0
C22 A:4WI401 1.3 26.0 1.0
F3 A:4WI401 2.1 27.1 1.0
F1 A:4WI401 2.1 26.2 1.0
C21 A:4WI401 2.4 24.4 1.0
O A:HOH528 2.7 26.5 1.0
HD3 A:PRO168 2.8 23.2 1.0
H16 A:4WI401 2.8 22.6 1.0
N4 A:4WI401 3.0 22.6 1.0
HA A:LEU167 3.2 20.4 1.0
O4 A:4WI401 3.3 25.4 1.0
O A:GLU166 3.6 17.7 1.0
CD A:PRO168 3.7 23.4 1.0
HD23 A:LEU167 3.7 21.3 1.0
H A:GLN192 4.0 18.4 1.0
HG3 A:PRO168 4.0 23.1 1.0
H17 A:4WI401 4.1 20.9 1.0
CA A:LEU167 4.1 20.4 1.0
HD2 A:PRO168 4.2 23.2 1.0
O A:GLN192 4.3 17.4 1.0
HE3 A:MET165 4.3 16.9 1.0
N A:PRO168 4.4 22.7 1.0
C14 A:4WI401 4.4 21.2 1.0
O A:HOH615 4.4 24.8 1.0
HG3 A:GLN192 4.4 15.5 1.0
CG A:PRO168 4.4 23.2 1.0
C A:LEU167 4.6 21.7 1.0
C A:GLU166 4.6 17.7 1.0
H15 A:4WI401 4.6 21.1 1.0
O A:THR190 4.6 23.7 1.0
H19 A:4WI401 4.7 20.9 1.0
CD2 A:LEU167 4.7 21.4 1.0
HB2 A:GLN192 4.7 16.2 1.0
C16 A:4WI401 4.8 20.9 1.0
N A:LEU167 4.8 18.9 1.0
N A:GLN192 4.9 18.2 1.0
HA A:ALA191 4.9 20.9 1.0
H29 A:4WI401 4.9 20.4 1.0
HA A:GLN189 5.0 21.6 1.0

Fluorine binding site 3 out of 6 in 8e26

Go back to Fluorine Binding Sites List in 8e26
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir


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 N142S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.1
occ:1.00
 F3 A:4WI401 0.0 27.1 1.0
C22 A:4WI401 1.3 26.0 1.0
F1 A:4WI401 2.1 26.2 1.0
F2 A:4WI401 2.1 25.8 1.0
C21 A:4WI401 2.4 24.4 1.0
O4 A:4WI401 2.6 25.4 1.0
HG3 A:GLN192 2.9 15.5 1.0
HE22 A:GLN192 3.0 14.8 1.0
O A:THR190 3.2 23.7 1.0
HE3 A:MET165 3.2 16.9 1.0
O A:HOH528 3.3 26.5 1.0
NE2 A:GLN192 3.5 14.8 1.0
HA A:GLN189 3.6 21.6 1.0
N4 A:4WI401 3.6 22.6 1.0
O A:ARG188 3.7 16.3 1.0
CG A:GLN192 3.7 15.6 1.0
H A:GLN192 3.8 18.4 1.0
H16 A:4WI401 3.8 22.6 1.0
CD A:GLN192 3.9 14.8 1.0
HE1 A:MET165 3.9 16.9 1.0
HB2 A:GLN192 4.0 16.2 1.0
CE A:MET165 4.0 16.9 1.0
HD23 A:LEU167 4.0 21.3 1.0
HE21 A:GLN192 4.0 14.8 1.0
CB A:GLN192 4.4 16.1 1.0
N A:GLN192 4.4 18.2 1.0
C A:THR190 4.4 22.8 1.0
CA A:GLN189 4.4 21.6 1.0
HD3 A:PRO168 4.5 23.2 1.0
HG2 A:GLN192 4.5 15.5 1.0
C A:GLN189 4.5 22.9 1.0
HE2 A:MET165 4.5 16.9 1.0
HA A:LEU167 4.6 20.4 1.0
N A:THR190 4.7 23.4 1.0
HA A:ALA191 4.7 20.9 1.0
C A:ARG188 4.7 16.6 1.0
H A:THR190 4.8 23.1 1.0
O A:GLN192 4.8 17.4 1.0
H15 A:4WI401 4.8 21.1 1.0
C14 A:4WI401 4.8 21.2 1.0
H25 A:4WI401 4.8 17.4 1.0
O A:GLU166 4.9 17.7 1.0
O A:GLN189 4.9 25.3 1.0
CA A:GLN192 4.9 17.3 1.0
OE1 A:GLN192 4.9 13.4 1.0
CD2 A:LEU167 4.9 21.4 1.0
HG2 A:GLN189 5.0 24.2 1.0
O A:HOH615 5.0 24.8 1.0
HB2 A:MET165 5.0 14.0 1.0

Fluorine binding site 4 out of 6 in 8e26

Go back to Fluorine Binding Sites List in 8e26
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir


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 N142S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:51.8
occ:1.00
 F1 B:4WI401 0.0 51.8 1.0
C22 B:4WI401 1.3 46.6 1.0
F3 B:4WI401 2.1 47.4 1.0
F2 B:4WI401 2.1 45.6 1.0
C21 B:4WI401 2.4 42.0 1.0
H16 B:4WI401 2.6 36.8 1.0
HD3 B:PRO168 2.8 20.0 1.0
N4 B:4WI401 2.9 36.6 1.0
HA B:LEU167 3.1 19.1 1.0
O4 B:4WI401 3.3 42.2 1.0
O B:GLU166 3.5 17.4 1.0
HD23 B:LEU167 3.5 19.8 1.0
CD B:PRO168 3.7 20.1 1.0
HB2 B:GLN192 3.8 16.4 1.0
CA B:LEU167 4.0 19.1 1.0
H B:GLN192 4.1 18.8 1.0
O B:GLN192 4.1 17.7 1.0
H29 B:4WI401 4.1 31.6 1.0
HD2 B:PRO168 4.2 20.0 1.0
N B:PRO168 4.2 19.6 1.0
C14 B:4WI401 4.3 33.0 1.0
O B:THR190 4.3 23.5 1.0
C B:LEU167 4.4 19.4 1.0
CD2 B:LEU167 4.4 19.8 1.0
C B:GLU166 4.4 17.2 1.0
H15 B:4WI401 4.5 33.1 1.0
HD21 B:LEU167 4.5 19.8 1.0
HG3 B:PRO168 4.6 20.4 1.0
H31 B:4WI401 4.6 31.5 1.0
H20 B:4WI401 4.6 31.1 1.0
CB B:GLN192 4.7 16.5 1.0
N B:GLN192 4.7 18.7 1.0
N B:LEU167 4.7 18.3 1.0
CG B:PRO168 4.7 20.5 1.0
C23 B:4WI401 4.7 31.5 1.0
HB3 B:PRO168 4.8 20.3 1.0
H21 B:4WI401 4.9 31.1 1.0
HA B:ALA191 4.9 21.9 1.0
C15 B:4WI401 4.9 31.8 1.0
HD22 B:LEU167 5.0 19.8 1.0
HG3 B:GLN192 5.0 15.5 1.0
C B:GLN192 5.0 17.5 1.0
HA B:PRO168 5.0 19.9 1.0

Fluorine binding site 5 out of 6 in 8e26

Go back to Fluorine Binding Sites List in 8e26
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir


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 N142S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:45.6
occ:1.00
 F2 B:4WI401 0.0 45.6 1.0
C22 B:4WI401 1.3 46.6 1.0
F1 B:4WI401 2.1 51.8 1.0
F3 B:4WI401 2.1 47.4 1.0
C21 B:4WI401 2.4 42.0 1.0
HD23 B:LEU167 2.4 19.8 1.0
H16 B:4WI401 2.9 36.8 1.0
HA B:LEU167 2.9 19.1 1.0
N4 B:4WI401 3.0 36.6 1.0
O B:GLU166 3.1 17.4 1.0
O4 B:4WI401 3.2 42.2 1.0
CD2 B:LEU167 3.3 19.8 1.0
HB2 B:GLN192 3.4 16.4 1.0
SD B:MET165 3.6 19.7 1.0
HD22 B:LEU167 3.6 19.8 1.0
HB2 B:MET165 3.7 15.3 1.0
C B:GLU166 3.8 17.2 1.0
CA B:LEU167 3.8 19.1 1.0
HD21 B:LEU167 3.8 19.8 1.0
HD3 B:PRO168 4.0 20.0 1.0
HG B:LEU167 4.1 19.8 1.0
N B:LEU167 4.1 18.3 1.0
CG B:LEU167 4.2 19.7 1.0
HE22 B:GLN192 4.3 14.0 1.0
CB B:GLN192 4.3 16.5 1.0
HG3 B:MET165 4.3 16.9 1.0
C14 B:4WI401 4.4 33.0 1.0
CG B:MET165 4.4 16.5 1.0
NE2 B:GLN192 4.5 13.9 1.0
CB B:MET165 4.5 15.3 1.0
H B:GLU166 4.5 15.1 1.0
CB B:LEU167 4.6 19.8 1.0
HB3 B:GLN192 4.6 16.4 1.0
H15 B:4WI401 4.7 33.1 1.0
C13 B:4WI401 4.7 31.5 1.0
HE21 B:GLN192 4.7 14.0 1.0
N B:GLU166 4.7 15.0 1.0
HG3 B:GLN192 4.7 15.5 1.0
CD B:PRO168 4.7 20.1 1.0
CD B:GLN192 4.8 14.4 1.0
O B:GLN192 4.8 17.7 1.0
HD2 B:PRO168 4.8 20.0 1.0
H20 B:4WI401 4.8 31.1 1.0
O3 B:4WI401 4.8 32.0 1.0
C B:LEU167 4.9 19.4 1.0
H B:LEU167 4.9 18.2 1.0
CG B:GLN192 4.9 15.5 1.0
HB3 B:LEU167 4.9 19.6 1.0
CA B:GLU166 4.9 15.8 1.0
O B:THR190 4.9 23.5 1.0
H26 B:4WI401 5.0 25.4 1.0

Fluorine binding site 6 out of 6 in 8e26

Go back to Fluorine Binding Sites List in 8e26
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir


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 N142S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:47.4
occ:1.00
 F3 B:4WI401 0.0 47.4 1.0
C22 B:4WI401 1.3 46.6 1.0
F1 B:4WI401 2.1 51.8 1.0
F2 B:4WI401 2.1 45.6 1.0
C21 B:4WI401 2.4 42.0 1.0
O4 B:4WI401 2.6 42.2 1.0
O B:THR190 2.8 23.5 1.0
HB2 B:GLN192 2.8 16.4 1.0
HE22 B:GLN192 3.0 14.0 1.0
HG3 B:GLN192 3.2 15.5 1.0
N4 B:4WI401 3.6 36.6 1.0
NE2 B:GLN192 3.6 13.9 1.0
CB B:GLN192 3.6 16.5 1.0
CG B:GLN192 3.7 15.5 1.0
H B:GLN192 3.8 18.8 1.0
H16 B:4WI401 3.8 36.8 1.0
HD23 B:LEU167 3.9 19.8 1.0
H B:THR190 4.0 27.8 1.0
CD B:GLN192 4.0 14.4 1.0
N B:GLN192 4.0 18.7 1.0
C B:THR190 4.1 25.2 1.0
HE21 B:GLN192 4.1 14.0 1.0
O B:ARG188 4.2 28.9 1.0
HA B:GLN189 4.3 30.8 1.0
HB3 B:GLN192 4.3 16.4 1.0
CA B:GLN192 4.4 17.3 1.0
HD3 B:PRO168 4.4 20.0 1.0
HA B:ALA191 4.4 21.9 1.0
N B:THR190 4.5 27.8 1.0
O B:GLN192 4.5 17.7 1.0
HA B:LEU167 4.5 19.1 1.0
C B:ALA191 4.6 20.3 1.0
HG2 B:GLN192 4.6 15.4 1.0
SD B:MET165 4.7 19.7 1.0
CD2 B:LEU167 4.7 19.8 1.0
H15 B:4WI401 4.7 33.1 1.0
C14 B:4WI401 4.8 33.0 1.0
HD22 B:LEU167 4.8 19.8 1.0
HD21 B:LEU167 4.9 19.8 1.0
O B:GLU166 4.9 17.4 1.0
CA B:ALA191 4.9 21.9 1.0
N B:ALA191 4.9 23.4 1.0
C B:GLN192 4.9 17.5 1.0
CA B:THR190 5.0 26.4 1.0

Reference:

G.D.Noske, A.S.Godoy, G.Oliva. Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir To Be Published.
Page generated: Fri Aug 2 17:47:35 2024

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