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Fluorine in PDB 8dza: Crystal Structure of Sars-Cov-2 Main Protease A193T Mutant in Complex with Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease A193T Mutant in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease A193T Mutant in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease A193T Mutant in Complex with Nirmatrelvir, PDB code: 8dza 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) 72.06 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.989, 99.979, 103.638, 90, 90, 90
R / Rfree (%) 20.1 / 24.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease A193T Mutant in Complex with Nirmatrelvir (pdb code 8dza). 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 A193T Mutant in Complex with Nirmatrelvir, PDB code: 8dza:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8dza

Go back to Fluorine Binding Sites List in 8dza
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193T 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 A193T Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:49.4
occ:1.00
 F1 A:4WI402 0.0 49.4 1.0
C22 A:4WI402 1.3 53.7 1.0
F2 A:4WI402 2.1 53.5 1.0
F3 A:4WI402 2.2 56.6 1.0
C21 A:4WI402 2.4 48.7 1.0
H16 A:4WI402 2.6 45.4 1.0
HD3 A:PRO168 2.8 39.9 1.0
N4 A:4WI402 2.9 44.7 1.0
HA A:LEU167 2.9 32.2 1.0
O A:GLU166 3.3 30.9 1.0
O4 A:4WI402 3.3 46.5 1.0
HD13 A:LEU167 3.4 32.5 1.0
HG3 A:PRO168 3.5 39.4 1.0
O A:HOH564 3.5 35.6 1.0
CD A:PRO168 3.7 40.4 1.0
CA A:LEU167 3.8 32.2 1.0
CG A:PRO168 4.1 39.1 1.0
HD11 A:LEU167 4.1 32.5 1.0
N A:PRO168 4.1 39.9 1.0
H29 A:4WI402 4.1 42.0 1.0
C A:GLU166 4.1 30.8 1.0
CD1 A:LEU167 4.2 32.9 1.0
HB2 A:GLN192 4.2 36.3 1.0
C A:LEU167 4.2 35.1 1.0
H A:GLN192 4.3 38.6 1.0
C14 A:4WI402 4.3 43.7 1.0
N A:LEU167 4.4 30.2 1.0
HD2 A:PRO168 4.4 39.9 1.0
O A:GLN192 4.4 33.7 1.0
H15 A:4WI402 4.5 43.5 1.0
O A:THR190 4.5 42.5 1.0
HG2 A:PRO168 4.6 39.4 1.0
H31 A:4WI402 4.6 42.0 1.0
C23 A:4WI402 4.7 41.9 1.0
H17 A:4WI402 4.7 42.0 1.0
HD12 A:LEU167 4.8 32.5 1.0
CB A:LEU167 4.9 31.5 1.0
HA A:PRO168 4.9 39.2 1.0
HE22 A:GLN192 4.9 32.2 1.0
C15 A:4WI402 5.0 42.6 1.0

Fluorine binding site 2 out of 6 in 8dza

Go back to Fluorine Binding Sites List in 8dza
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193T 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 A193T Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:53.5
occ:1.00
 F2 A:4WI402 0.0 53.5 1.0
C22 A:4WI402 1.3 53.7 1.0
F3 A:4WI402 2.1 56.6 1.0
F1 A:4WI402 2.1 49.4 1.0
C21 A:4WI402 2.4 48.7 1.0
O4 A:4WI402 2.6 46.5 1.0
HE22 A:GLN192 2.9 32.2 1.0
O A:THR190 3.0 42.5 1.0
HB2 A:GLN192 3.3 36.3 1.0
NE2 A:GLN192 3.5 31.5 1.0
N4 A:4WI402 3.6 44.7 1.0
HA A:GLN189 3.7 40.0 1.0
HD13 A:LEU167 3.7 32.5 1.0
HG3 A:GLN192 3.8 35.3 1.0
H16 A:4WI402 3.8 45.4 1.0
HE21 A:GLN192 3.9 32.2 1.0
H A:GLN192 3.9 38.6 1.0
O A:ARG188 4.0 29.7 1.0
H A:THR190 4.1 43.8 1.0
CB A:GLN192 4.1 36.4 1.0
C A:THR190 4.2 45.0 1.0
CG A:GLN192 4.2 35.5 1.0
CD A:GLN192 4.2 34.1 1.0
HD3 A:PRO168 4.3 39.9 1.0
HA A:LEU167 4.3 32.2 1.0
N A:THR190 4.3 43.9 1.0
N A:GLN192 4.4 38.1 1.0
CD1 A:LEU167 4.4 32.9 1.0
HD11 A:LEU167 4.4 32.5 1.0
HG2 A:GLN189 4.4 50.9 1.0
SD A:MET165 4.5 39.4 1.0
CA A:GLN189 4.5 39.8 1.0
HD12 A:LEU167 4.6 32.5 1.0
C A:GLN189 4.7 43.0 1.0
H15 A:4WI402 4.7 43.5 1.0
HB3 A:GLN192 4.8 36.3 1.0
O A:GLU166 4.8 30.9 1.0
C14 A:4WI402 4.8 43.7 1.0
CA A:GLN192 4.8 37.1 1.0
O A:GLN192 4.8 33.7 1.0
HA A:ALA191 4.8 43.9 1.0
H28 A:4WI402 4.9 42.3 1.0
HB2 A:MET165 4.9 30.6 1.0
H11 A:4WI402 4.9 43.8 1.0
CA A:THR190 5.0 44.7 1.0
C A:ARG188 5.0 32.2 1.0

Fluorine binding site 3 out of 6 in 8dza

Go back to Fluorine Binding Sites List in 8dza
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193T 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 A193T Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:56.6
occ:1.00
 F3 A:4WI402 0.0 56.6 1.0
C22 A:4WI402 1.3 53.7 1.0
F2 A:4WI402 2.1 53.5 1.0
F1 A:4WI402 2.2 49.4 1.0
C21 A:4WI402 2.4 48.7 1.0
HD13 A:LEU167 2.5 32.5 1.0
H16 A:4WI402 2.8 45.4 1.0
N4 A:4WI402 2.9 44.7 1.0
HA A:LEU167 3.0 32.2 1.0
O A:GLU166 3.1 30.9 1.0
HB2 A:MET165 3.2 30.6 1.0
O4 A:4WI402 3.2 46.5 1.0
SD A:MET165 3.4 39.4 1.0
CD1 A:LEU167 3.5 32.9 1.0
C A:GLU166 3.6 30.8 1.0
HD12 A:LEU167 3.8 32.5 1.0
CA A:LEU167 3.9 32.2 1.0
HD11 A:LEU167 3.9 32.5 1.0
HD21 A:LEU167 3.9 33.5 1.0
N A:LEU167 3.9 30.2 1.0
HB2 A:GLN192 4.0 36.3 1.0
CB A:MET165 4.0 30.9 1.0
HD3 A:PRO168 4.0 39.9 1.0
HE22 A:GLN192 4.1 32.2 1.0
H A:GLU166 4.2 26.9 1.0
CG A:MET165 4.2 34.1 1.0
C14 A:4WI402 4.2 43.7 1.0
HG3 A:MET165 4.2 34.4 1.0
NE2 A:GLN192 4.4 31.5 1.0
N A:GLU166 4.4 26.2 1.0
CG A:LEU167 4.4 31.6 1.0
HE21 A:GLN192 4.4 32.2 1.0
HB3 A:MET165 4.5 30.6 1.0
C13 A:4WI402 4.5 42.8 1.0
CD2 A:LEU167 4.5 34.4 1.0
H15 A:4WI402 4.6 43.5 1.0
H A:LEU167 4.6 30.8 1.0
O3 A:4WI402 4.6 41.7 1.0
H26 A:4WI402 4.6 42.3 1.0
CA A:GLU166 4.7 30.3 1.0
CB A:LEU167 4.7 31.5 1.0
HD22 A:LEU167 4.7 33.5 1.0
H17 A:4WI402 4.8 42.0 1.0
C A:MET165 4.9 25.1 1.0
O A:HOH564 4.9 35.6 1.0
C A:LEU167 4.9 35.1 1.0
H28 A:4WI402 5.0 42.3 1.0
CD A:PRO168 5.0 40.4 1.0
CB A:GLN192 5.0 36.4 1.0
HA A:GLN189 5.0 40.0 1.0
CE A:MET165 5.0 42.7 1.0

Fluorine binding site 4 out of 6 in 8dza

Go back to Fluorine Binding Sites List in 8dza
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193T 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 A193T Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:75.3
occ:1.00
 F1 B:4WI401 0.0 75.3 1.0
C22 B:4WI401 1.3 76.2 1.0
F2 B:4WI401 2.1 86.7 1.0
F3 B:4WI401 2.1 85.0 1.0
HE2 B:MET165 2.3 47.8 1.0
C21 B:4WI401 2.4 69.5 1.0
HD23 B:LEU167 2.7 41.8 1.0
H16 B:4WI401 2.7 61.5 1.0
N4 B:4WI401 2.9 61.9 1.0
O B:GLU166 3.1 40.3 1.0
HA B:LEU167 3.1 42.7 1.0
CE B:MET165 3.3 48.5 1.0
O4 B:4WI401 3.3 68.7 1.0
HD3 B:PRO168 3.5 54.3 1.0
CD2 B:LEU167 3.6 41.9 1.0
HE1 B:MET165 3.6 47.8 1.0
HB2 B:MET165 3.7 37.4 1.0
HG3 B:GLN192 3.8 41.3 1.0
HE3 B:MET165 3.8 47.7 1.0
HG3 B:MET165 3.8 40.9 1.0
C B:GLU166 3.9 39.6 1.0
HD21 B:LEU167 3.9 41.8 1.0
HD22 B:LEU167 3.9 41.8 1.0
CA B:LEU167 4.0 42.2 1.0
HE22 B:GLN192 4.1 39.9 1.0
SD B:MET165 4.2 46.2 1.0
HB2 B:GLN192 4.2 42.1 1.0
N B:LEU167 4.3 41.4 1.0
C14 B:4WI401 4.3 53.9 1.0
CG B:MET165 4.3 40.6 1.0
NE2 B:GLN192 4.4 39.4 1.0
CB B:MET165 4.5 36.9 1.0
H B:GLN192 4.5 45.1 1.0
CD B:PRO168 4.5 54.8 1.0
CG B:GLN192 4.5 41.2 1.0
CD B:GLN192 4.6 41.1 1.0
CG B:LEU167 4.6 41.6 1.0
HG B:LEU167 4.6 42.0 1.0
H15 B:4WI401 4.6 54.8 1.0
H B:GLU166 4.7 36.1 1.0
O B:THR190 4.7 53.0 1.0
HE21 B:GLN192 4.7 39.9 1.0
C13 B:4WI401 4.8 54.1 1.0
H29 B:4WI401 4.8 48.4 1.0
CB B:LEU167 4.8 41.9 1.0
H20 B:4WI401 4.8 49.8 1.0
CB B:GLN192 4.8 41.7 1.0
N B:GLU166 4.8 36.1 1.0
HD2 B:PRO168 4.9 54.2 1.0
H11 B:4WI401 4.9 53.2 1.0
O B:GLN192 4.9 49.0 1.0
C B:LEU167 4.9 46.1 1.0
O3 B:4WI401 5.0 53.0 1.0
HB3 B:MET165 5.0 37.4 1.0
HG3 B:PRO168 5.0 56.5 1.0

Fluorine binding site 5 out of 6 in 8dza

Go back to Fluorine Binding Sites List in 8dza
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193T 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 A193T Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:86.7
occ:1.00
 F2 B:4WI401 0.0 86.7 1.0
C22 B:4WI401 1.3 76.2 1.0
F1 B:4WI401 2.1 75.3 1.0
F3 B:4WI401 2.1 85.0 1.0
HD3 B:PRO168 2.4 54.3 1.0
C21 B:4WI401 2.4 69.5 1.0
H16 B:4WI401 2.7 61.5 1.0
N4 B:4WI401 2.9 61.9 1.0
HA B:LEU167 3.0 42.7 1.0
HG3 B:PRO168 3.1 56.5 1.0
O B:GLU166 3.1 40.3 1.0
CD B:PRO168 3.2 54.8 1.0
O4 B:4WI401 3.3 68.7 1.0
H29 B:4WI401 3.6 48.4 1.0
CG B:PRO168 3.6 56.9 1.0
N B:PRO168 3.8 50.8 1.0
HD23 B:LEU167 3.8 41.8 1.0
CA B:LEU167 3.9 42.2 1.0
HD2 B:PRO168 3.9 54.2 1.0
H B:GLN192 4.0 45.1 1.0
H31 B:4WI401 4.0 48.4 1.0
HG2 B:PRO168 4.1 56.5 1.0
C B:LEU167 4.1 46.1 1.0
C B:GLU166 4.2 39.6 1.0
C23 B:4WI401 4.2 47.2 1.0
C14 B:4WI401 4.2 53.9 1.0
HE2 B:MET165 4.3 47.8 1.0
O B:GLN192 4.4 49.0 1.0
N B:LEU167 4.5 41.4 1.0
HG3 B:GLN192 4.5 41.3 1.0
HA B:PRO168 4.5 54.0 1.0
H15 B:4WI401 4.5 54.8 1.0
H20 B:4WI401 4.5 49.8 1.0
H21 B:4WI401 4.5 49.7 1.0
O B:THR190 4.6 53.0 1.0
CD2 B:LEU167 4.6 41.9 1.0
CA B:PRO168 4.6 54.4 1.0
C15 B:4WI401 4.7 51.2 1.0
HD21 B:LEU167 4.7 41.8 1.0
HA B:ALA191 4.7 47.4 1.0
CB B:PRO168 4.8 57.3 1.0
C17 B:4WI401 4.8 49.2 1.0
N B:GLN192 4.8 45.8 1.0
HB3 B:LEU167 5.0 41.9 1.0
CB B:LEU167 5.0 41.9 1.0

Fluorine binding site 6 out of 6 in 8dza

Go back to Fluorine Binding Sites List in 8dza
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193T 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 A193T Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:85.0
occ:1.00
 F3 B:4WI401 0.0 85.0 1.0
C22 B:4WI401 1.3 76.2 1.0
F1 B:4WI401 2.1 75.3 1.0
F2 B:4WI401 2.1 86.7 1.0
C21 B:4WI401 2.4 69.5 1.0
O4 B:4WI401 2.6 68.7 1.0
O B:THR190 2.7 53.0 1.0
HG3 B:GLN192 2.8 41.3 1.0
H B:GLN192 3.1 45.1 1.0
HE22 B:GLN192 3.4 39.9 1.0
N4 B:4WI401 3.6 61.9 1.0
HE2 B:MET165 3.6 47.8 1.0
HA B:ALA191 3.6 47.4 1.0
CG B:GLN192 3.7 41.2 1.0
N B:GLN192 3.8 45.8 1.0
H16 B:4WI401 3.8 61.5 1.0
HD3 B:PRO168 3.8 54.3 1.0
C B:THR190 3.9 53.7 1.0
NE2 B:GLN192 4.0 39.4 1.0
HB2 B:GLN192 4.1 42.1 1.0
HD23 B:LEU167 4.2 41.8 1.0
HE1 B:MET165 4.2 47.8 1.0
CD B:GLN192 4.3 41.1 1.0
HG2 B:GLN192 4.3 41.3 1.0
CA B:ALA191 4.3 47.6 1.0
CB B:GLN192 4.3 41.7 1.0
CE B:MET165 4.3 48.5 1.0
C B:ALA191 4.4 44.7 1.0
O B:ARG188 4.4 45.1 1.0
HA B:GLN189 4.5 54.4 1.0
HG3 B:PRO168 4.5 56.5 1.0
H29 B:4WI401 4.5 48.4 1.0
HA B:LEU167 4.5 42.7 1.0
O B:GLN192 4.5 49.0 1.0
N B:ALA191 4.6 50.6 1.0
CA B:GLN192 4.6 43.9 1.0
HE21 B:GLN192 4.7 39.9 1.0
CD B:PRO168 4.7 54.8 1.0
O B:GLU166 4.7 40.3 1.0
H15 B:4WI401 4.8 54.8 1.0
C B:GLN189 4.8 57.2 1.0
N B:THR190 4.8 58.8 1.0
C14 B:4WI401 4.8 53.9 1.0
HE3 B:MET165 4.9 47.7 1.0
HD21 B:LEU167 4.9 41.8 1.0
CG B:PRO168 5.0 56.9 1.0
CD2 B:LEU167 5.0 41.9 1.0
O B:GLN189 5.0 63.4 1.0

Reference:

G.D.Noske, G.Oliva, A.S.Godoy. Crystal Structure of Sars-Cov-2 Main Protease A193T Mutant in Complex with Nirmatrelvir To Be Published.
Page generated: Fri Aug 2 17:41:39 2024

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