Fluorine in PDB 8dz2: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Nirmatrelvir

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

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

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 8dz2 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) 70.70 / 2.13
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.319, 97.536, 102.327, 90, 90, 90
R / Rfree (%) 18.9 / 23

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Nirmatrelvir (pdb code 8dz2). 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 Nirmatrelvir, PDB code: 8dz2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8dz2

Go back to Fluorine Binding Sites List in 8dz2
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:49.0
occ:1.00
 F1 A:4WI401 0.0 49.0 1.0
C22 A:4WI401 1.3 45.7 1.0
HE2 A:MET165 2.0 42.7 1.0
F3 A:4WI401 2.1 42.1 1.0
F2 A:4WI401 2.2 45.0 1.0
C21 A:4WI401 2.3 39.4 1.0
HD23 A:LEU167 2.7 31.1 1.0
H16 A:4WI401 2.7 38.2 1.0
N4 A:4WI401 2.8 37.8 1.0
CE A:MET165 2.8 42.5 1.0
O A:GLU166 3.0 27.9 1.0
HE3 A:MET165 3.0 42.5 1.0
HA A:LEU167 3.0 30.4 1.0
HB2 A:MET165 3.2 33.5 1.0
HE1 A:MET165 3.2 42.6 1.0
O4 A:4WI401 3.3 39.4 1.0
CD2 A:LEU167 3.5 31.3 1.0
C A:GLU166 3.6 30.2 1.0
HD22 A:LEU167 3.7 31.1 1.0
HG A:LEU167 3.8 31.1 1.0
CA A:LEU167 3.9 30.0 1.0
HB2 A:GLN192 3.9 35.0 1.0
N A:LEU167 4.0 28.7 1.0
HG3 A:MET165 4.0 38.5 1.0
CB A:MET165 4.1 33.5 1.0
CG A:LEU167 4.1 30.7 1.0
C14 A:4WI401 4.2 38.0 1.0
HD3 A:PRO168 4.2 39.0 1.0
SD A:MET165 4.2 43.2 1.0
HD21 A:LEU167 4.2 31.1 1.0
CG A:MET165 4.3 39.1 1.0
H A:GLU166 4.3 27.6 1.0
O A:HOH593 4.4 47.8 1.0
HE22 A:GLN192 4.4 33.3 1.0
HB3 A:MET165 4.5 33.5 1.0
N A:GLU166 4.5 26.9 1.0
C13 A:4WI401 4.5 36.8 1.0
NE2 A:GLN192 4.5 33.6 1.0
H15 A:4WI401 4.5 36.9 1.0
O3 A:4WI401 4.5 38.4 1.0
CB A:LEU167 4.6 30.0 1.0
HE21 A:GLN192 4.7 33.3 1.0
H23 A:4WI401 4.7 33.6 1.0
CA A:GLU166 4.7 28.8 1.0
H29 A:4WI401 4.7 35.2 1.0
H A:LEU167 4.7 29.4 1.0
CB A:GLN192 4.9 35.0 1.0
HB3 A:LEU167 4.9 30.2 1.0
H17 A:4WI401 5.0 34.3 1.0
C A:MET165 5.0 27.8 1.0

Fluorine binding site 2 out of 6 in 8dz2

Go back to Fluorine Binding Sites List in 8dz2
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:45.0
occ:1.00
 F2 A:4WI401 0.0 45.0 1.0
C22 A:4WI401 1.3 45.7 1.0
F1 A:4WI401 2.2 49.0 1.0
F3 A:4WI401 2.2 42.1 1.0
C21 A:4WI401 2.4 39.4 1.0
O4 A:4WI401 2.6 39.4 1.0
HE2 A:MET165 3.0 42.7 1.0
HE22 A:GLN192 3.1 33.3 1.0
HB2 A:GLN192 3.1 35.0 1.0
O A:THR190 3.2 38.2 1.0
HE1 A:MET165 3.3 42.6 1.0
CE A:MET165 3.5 42.5 1.0
N4 A:4WI401 3.6 37.8 1.0
NE2 A:GLN192 3.6 33.6 1.0
HD23 A:LEU167 3.6 31.1 1.0
HA A:GLN189 3.7 36.7 1.0
HE3 A:MET165 3.7 42.5 1.0
H16 A:4WI401 3.8 38.2 1.0
HG3 A:GLN192 3.9 33.6 1.0
H A:GLN192 3.9 35.8 1.0
HE21 A:GLN192 4.0 33.3 1.0
CB A:GLN192 4.0 35.0 1.0
O A:ARG188 4.0 30.2 1.0
CD A:GLN192 4.2 32.7 1.0
CG A:GLN192 4.2 33.5 1.0
C A:THR190 4.4 39.7 1.0
N A:GLN192 4.4 35.5 1.0
HA A:LEU167 4.4 30.4 1.0
CD2 A:LEU167 4.5 31.3 1.0
CA A:GLN189 4.5 36.8 1.0
HG3 A:GLN189 4.5 43.5 1.0
HD3 A:PRO168 4.5 39.0 1.0
O A:GLN192 4.5 40.9 1.0
C A:GLN189 4.6 38.6 1.0
H A:THR190 4.6 39.2 1.0
N A:THR190 4.6 39.8 1.0
HD22 A:LEU167 4.6 31.1 1.0
HB3 A:GLN192 4.7 35.0 1.0
CA A:GLN192 4.7 36.4 1.0
O A:GLU166 4.7 27.9 1.0
H15 A:4WI401 4.7 36.9 1.0
C14 A:4WI401 4.8 38.0 1.0
HD21 A:LEU167 4.9 31.1 1.0
H17 A:4WI401 4.9 34.3 1.0
HB2 A:MET165 4.9 33.5 1.0
H25 A:4WI401 4.9 33.6 1.0
HA A:ALA191 5.0 38.2 1.0

Fluorine binding site 3 out of 6 in 8dz2

Go back to Fluorine Binding Sites List in 8dz2
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.1
occ:1.00
 F3 A:4WI401 0.0 42.1 1.0
C22 A:4WI401 1.3 45.7 1.0
F1 A:4WI401 2.1 49.0 1.0
F2 A:4WI401 2.2 45.0 1.0
C21 A:4WI401 2.4 39.4 1.0
H16 A:4WI401 2.7 38.2 1.0
HA A:LEU167 2.8 30.4 1.0
N4 A:4WI401 2.9 37.8 1.0
HD3 A:PRO168 3.0 39.0 1.0
O A:HOH593 3.0 47.8 1.0
O A:GLU166 3.3 27.9 1.0
O4 A:4WI401 3.3 39.4 1.0
HD23 A:LEU167 3.3 31.1 1.0
HG3 A:PRO168 3.7 40.2 1.0
CA A:LEU167 3.8 30.0 1.0
CD A:PRO168 3.8 39.2 1.0
H17 A:4WI401 4.0 34.3 1.0
HE2 A:MET165 4.0 42.7 1.0
HB2 A:GLN192 4.1 35.0 1.0
O A:HOH654 4.1 49.1 1.0
O A:GLN192 4.2 40.9 1.0
C A:GLU166 4.2 30.2 1.0
CD2 A:LEU167 4.3 31.3 1.0
N A:PRO168 4.3 36.9 1.0
CG A:PRO168 4.3 41.1 1.0
C14 A:4WI401 4.3 38.0 1.0
C A:LEU167 4.3 33.4 1.0
H A:GLN192 4.4 35.8 1.0
N A:LEU167 4.4 28.7 1.0
H19 A:4WI401 4.5 34.3 1.0
HD2 A:PRO168 4.6 39.0 1.0
H15 A:4WI401 4.6 36.9 1.0
HD21 A:LEU167 4.6 31.1 1.0
C16 A:4WI401 4.6 34.5 1.0
CB A:LEU167 4.7 30.0 1.0
HD22 A:LEU167 4.8 31.1 1.0
CE A:MET165 4.8 42.5 1.0
HG2 A:PRO168 4.8 40.2 1.0
HB3 A:LEU167 4.8 30.2 1.0
H29 A:4WI401 4.8 35.2 1.0
O A:THR190 4.8 38.2 1.0
HE3 A:MET165 4.8 42.5 1.0
HG A:LEU167 4.9 31.1 1.0
CG A:LEU167 4.9 30.7 1.0
HE1 A:MET165 4.9 42.6 1.0
C15 A:4WI401 5.0 33.7 1.0

Fluorine binding site 4 out of 6 in 8dz2

Go back to Fluorine Binding Sites List in 8dz2
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:64.2
occ:1.00
 F1 B:4WI401 0.0 64.2 1.0
C22 B:4WI401 1.3 57.3 1.0
F2 B:4WI401 2.1 61.0 1.0
F3 B:4WI401 2.1 61.3 1.0
C21 B:4WI401 2.4 51.8 1.0
O4 B:4WI401 2.6 52.2 1.0
O B:THR190 2.6 51.3 1.0
HE22 B:GLN192 2.8 38.7 1.0
HE2 B:MET165 3.1 45.6 1.0
HG3 B:GLN192 3.2 38.6 1.0
HB2 B:GLN192 3.2 39.5 1.0
HE3 B:MET165 3.3 45.6 1.0
HE1 B:MET165 3.4 45.6 1.0
H B:GLN192 3.4 42.5 1.0
H B:THR190 3.4 50.4 1.0
NE2 B:GLN192 3.4 39.1 1.0
CE B:MET165 3.5 47.1 1.0
N4 B:4WI401 3.5 45.2 1.0
HD23 B:LEU167 3.7 43.0 1.0
H16 B:4WI401 3.7 46.7 1.0
CG B:GLN192 3.8 38.7 1.0
C B:THR190 3.9 51.6 1.0
HD3 B:PRO168 3.9 50.7 1.0
CB B:GLN192 3.9 38.9 1.0
N B:GLN192 3.9 41.6 1.0
CD B:GLN192 3.9 38.0 1.0
HE21 B:GLN192 4.0 38.8 1.0
HA B:LEU167 4.2 38.7 1.0
N B:THR190 4.3 50.1 1.0
HA B:ALA191 4.3 51.2 1.0
O B:ARG188 4.4 39.7 1.0
CA B:GLN192 4.5 41.7 1.0
CD2 B:LEU167 4.5 43.6 1.0
C B:ALA191 4.6 45.4 1.0
O B:GLN192 4.7 45.0 1.0
HA B:GLN189 4.7 53.5 1.0
HD21 B:LEU167 4.7 43.0 1.0
HG2 B:GLN192 4.7 38.6 1.0
O B:GLU166 4.7 34.5 1.0
HG21 B:THR190 4.7 53.9 1.0
HB3 B:GLN192 4.7 39.5 1.0
HD22 B:LEU167 4.7 43.0 1.0
CA B:THR190 4.8 50.7 1.0
N B:ALA191 4.8 52.3 1.0
H15 B:4WI401 4.8 46.0 1.0
C14 B:4WI401 4.8 45.6 1.0
CA B:ALA191 4.8 52.3 1.0
CD B:PRO168 4.8 51.5 1.0
H25 B:4WI401 5.0 42.8 1.0
OE1 B:GLN192 5.0 36.6 1.0
HB2 B:MET165 5.0 35.7 1.0
H20 B:4WI401 5.0 42.4 1.0

Fluorine binding site 5 out of 6 in 8dz2

Go back to Fluorine Binding Sites List in 8dz2
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:61.0
occ:1.00
 F2 B:4WI401 0.0 61.0 1.0
C22 B:4WI401 1.3 57.3 1.0
F1 B:4WI401 2.1 64.2 1.0
F3 B:4WI401 2.1 61.3 1.0
C21 B:4WI401 2.4 51.8 1.0
HE2 B:MET165 2.4 45.6 1.0
H16 B:4WI401 2.5 46.7 1.0
HD23 B:LEU167 2.5 43.0 1.0
HA B:LEU167 2.7 38.7 1.0
N4 B:4WI401 2.8 45.2 1.0
O B:GLU166 2.8 34.5 1.0
HE3 B:MET165 2.8 45.6 1.0
CE B:MET165 3.0 47.1 1.0
O4 B:4WI401 3.4 52.2 1.0
C B:GLU166 3.4 34.4 1.0
HD3 B:PRO168 3.4 50.7 1.0
HB2 B:MET165 3.5 35.7 1.0
CD2 B:LEU167 3.5 43.6 1.0
HE1 B:MET165 3.5 45.6 1.0
CA B:LEU167 3.6 38.7 1.0
N B:LEU167 3.8 35.5 1.0
HD22 B:LEU167 3.8 43.0 1.0
HG3 B:MET165 3.9 39.9 1.0
HB2 B:GLN192 3.9 39.5 1.0
HD21 B:LEU167 4.0 43.0 1.0
HG B:LEU167 4.1 41.5 1.0
C14 B:4WI401 4.2 45.6 1.0
H B:GLU166 4.2 32.6 1.0
CG B:LEU167 4.3 41.5 1.0
HE22 B:GLN192 4.3 38.7 1.0
CB B:MET165 4.3 35.0 1.0
CG B:MET165 4.4 41.2 1.0
CD B:PRO168 4.4 51.5 1.0
N B:GLU166 4.4 32.0 1.0
CB B:LEU167 4.5 38.2 1.0
SD B:MET165 4.5 42.4 1.0
H B:LEU167 4.5 35.9 1.0
CA B:GLU166 4.6 35.1 1.0
H15 B:4WI401 4.6 46.0 1.0
C13 B:4WI401 4.6 49.5 1.0
C B:LEU167 4.6 42.4 1.0
NE2 B:GLN192 4.6 39.1 1.0
H29 B:4WI401 4.6 42.7 1.0
O3 B:4WI401 4.6 53.4 1.0
H B:GLN192 4.7 42.5 1.0
HD2 B:PRO168 4.7 50.7 1.0
O B:THR190 4.8 51.3 1.0
HB3 B:LEU167 4.8 39.1 1.0
HB3 B:MET165 4.8 35.7 1.0
N B:PRO168 4.9 48.5 1.0
CB B:GLN192 4.9 38.9 1.0
HG3 B:GLN192 4.9 38.6 1.0
H23 B:4WI401 4.9 42.8 1.0
H20 B:4WI401 4.9 42.4 1.0
HE21 B:GLN192 5.0 38.8 1.0

Fluorine binding site 6 out of 6 in 8dz2

Go back to Fluorine Binding Sites List in 8dz2
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:61.3
occ:1.00
 F3 B:4WI401 0.0 61.3 1.0
C22 B:4WI401 1.3 57.3 1.0
F1 B:4WI401 2.1 64.2 1.0
F2 B:4WI401 2.1 61.0 1.0
HD3 B:PRO168 2.3 50.7 1.0
C21 B:4WI401 2.4 51.8 1.0
H16 B:4WI401 3.0 46.7 1.0
HA B:LEU167 3.0 38.7 1.0
N4 B:4WI401 3.0 45.2 1.0
O4 B:4WI401 3.1 52.2 1.0
CD B:PRO168 3.2 51.5 1.0
HG3 B:PRO168 3.3 51.6 1.0
O B:GLU166 3.4 34.5 1.0
HD23 B:LEU167 3.6 43.0 1.0
H B:GLN192 3.7 42.5 1.0
CG B:PRO168 3.7 51.5 1.0
HD2 B:PRO168 3.9 50.7 1.0
CA B:LEU167 3.9 38.7 1.0
N B:PRO168 3.9 48.5 1.0
H20 B:4WI401 3.9 42.4 1.0
O B:THR190 4.0 51.3 1.0
HG2 B:PRO168 4.1 51.6 1.0
HB2 B:GLN192 4.3 39.5 1.0
C B:LEU167 4.3 42.4 1.0
O B:GLN192 4.3 45.0 1.0
C B:GLU166 4.3 34.4 1.0
HE2 B:MET165 4.4 45.6 1.0
C14 B:4WI401 4.4 45.6 1.0
HA B:ALA191 4.5 51.2 1.0
N B:GLN192 4.5 41.6 1.0
H22 B:4WI401 4.5 42.4 1.0
CD2 B:LEU167 4.5 43.6 1.0
N B:LEU167 4.6 35.5 1.0
C17 B:4WI401 4.6 41.7 1.0
H15 B:4WI401 4.6 46.0 1.0
HE3 B:MET165 4.6 45.6 1.0
HD21 B:LEU167 4.7 43.0 1.0
HA B:PRO168 4.7 49.4 1.0
CA B:PRO168 4.9 48.1 1.0
HG3 B:GLN192 4.9 38.6 1.0
CE B:MET165 4.9 47.1 1.0
HB3 B:LEU167 5.0 39.1 1.0
H B:THR190 5.0 50.4 1.0
HE22 B:GLN192 5.0 38.7 1.0
H29 B:4WI401 5.0 42.7 1.0
CB B:LEU167 5.0 38.2 1.0

Reference:

G.D.Noske, G.Oliva, A.S.Godoy. Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir To Be Published.
Page generated: Fri Aug 2 17:41:07 2024

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