Fluorine in PDB 8e1y: Crystal Structure of Sars-Cov-2 Main Protease A193S Mutant in Complex with Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease A193S Mutant in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease A193S Mutant in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease A193S Mutant in Complex with Nirmatrelvir, PDB code: 8e1y 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) 72.50 / 2.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.905, 103.925, 68.025, 90, 90, 90
R / Rfree (%) 21.7 / 27.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease A193S Mutant in Complex with Nirmatrelvir (pdb code 8e1y). 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 A193S Mutant in Complex with Nirmatrelvir, PDB code: 8e1y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8e1y

Go back to Fluorine Binding Sites List in 8e1y
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193S 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 A193S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:81.9
occ:1.00
 F1 A:4WI401 0.0 81.9 1.0
C22 A:4WI401 1.3 85.1 1.0
F2 A:4WI401 2.1 89.3 1.0
F3 A:4WI401 2.1 87.5 1.0
C21 A:4WI401 2.4 81.1 1.0
HE1 A:MET165 2.6 27.3 1.0
O4 A:4WI401 2.7 82.6 1.0
HG3 A:GLN192 2.7 40.9 1.0
HE22 A:GLN192 2.8 39.3 1.0
HG2 A:GLN192 3.1 40.9 1.0
CG A:GLN192 3.3 41.0 1.0
HE3 A:MET165 3.3 27.3 1.0
CE A:MET165 3.3 27.3 1.0
O A:THR190 3.4 50.3 1.0
HD23 A:LEU167 3.4 31.6 1.0
NE2 A:GLN192 3.5 39.1 1.0
N4 A:4WI401 3.5 74.6 1.0
HE2 A:MET165 3.6 27.2 1.0
H A:GLN192 3.7 45.5 1.0
H16 A:4WI401 3.7 75.1 1.0
HA A:GLN189 3.8 46.1 1.0
CD A:GLN192 3.8 39.8 1.0
O A:ARG188 4.0 34.1 1.0
HD3 A:PRO168 4.0 38.3 1.0
HA A:LEU167 4.2 32.2 1.0
HE21 A:GLN192 4.2 39.2 1.0
CD2 A:LEU167 4.3 31.6 1.0
H29 A:4WI401 4.4 71.5 1.0
HD22 A:LEU167 4.4 31.6 1.0
N A:GLN192 4.4 45.5 1.0
O A:GLN192 4.5 42.8 1.0
C A:THR190 4.5 51.9 1.0
HD21 A:LEU167 4.6 31.6 1.0
CB A:GLN192 4.6 42.1 1.0
CA A:GLN189 4.7 46.0 1.0
H15 A:4WI401 4.7 70.9 1.0
HA A:ALA191 4.8 51.3 1.0
C A:GLN189 4.8 48.5 1.0
C14 A:4WI401 4.8 71.4 1.0
HG3 A:GLN189 4.8 52.8 1.0
O A:GLU166 4.8 30.1 1.0
SD A:MET165 4.8 26.8 1.0
N A:THR190 4.9 51.0 1.0
HG3 A:PRO168 4.9 38.3 1.0
H25 A:4WI401 4.9 58.6 1.0
H A:THR190 4.9 50.5 1.0
CA A:GLN192 5.0 43.6 1.0
CD A:PRO168 5.0 38.8 1.0

Fluorine binding site 2 out of 6 in 8e1y

Go back to Fluorine Binding Sites List in 8e1y
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193S 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 A193S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:89.3
occ:1.00
 F2 A:4WI401 0.0 89.3 1.0
C22 A:4WI401 1.3 85.1 1.0
F1 A:4WI401 2.1 81.9 1.0
F3 A:4WI401 2.1 87.5 1.0
C21 A:4WI401 2.4 81.1 1.0
H29 A:4WI401 2.7 71.5 1.0
O4 A:4WI401 3.1 82.6 1.0
N4 A:4WI401 3.1 74.6 1.0
H16 A:4WI401 3.4 75.1 1.0
C23 A:4WI401 3.6 71.8 1.0
HG3 A:GLN189 3.6 52.8 1.0
H31 A:4WI401 3.7 71.5 1.0
HA A:GLN189 3.8 46.1 1.0
HG3 A:PRO168 3.9 38.3 1.0
H15 A:4WI401 3.9 70.9 1.0
O A:THR190 4.0 50.3 1.0
HD3 A:PRO168 4.0 38.3 1.0
C14 A:4WI401 4.1 71.4 1.0
H30 A:4WI401 4.1 71.5 1.0
H A:GLN192 4.3 45.5 1.0
C15 A:4WI401 4.5 71.3 1.0
HE1 A:MET165 4.5 27.3 1.0
HA A:ALA191 4.5 51.3 1.0
HG3 A:GLN192 4.5 40.9 1.0
O A:GLN189 4.5 50.5 1.0
HA A:LEU167 4.5 32.2 1.0
C A:GLN189 4.6 48.5 1.0
CG A:GLN189 4.6 52.6 1.0
CA A:GLN189 4.6 46.0 1.0
HE3 A:MET165 4.6 27.3 1.0
HG2 A:GLN192 4.6 40.9 1.0
CG A:PRO168 4.7 38.5 1.0
HE22 A:GLN192 4.7 39.3 1.0
C A:THR190 4.7 51.9 1.0
HD23 A:LEU167 4.7 31.6 1.0
CD A:PRO168 4.8 38.8 1.0
O A:GLU166 4.8 30.1 1.0
HG2 A:GLN189 4.8 52.8 1.0
HG2 A:PRO168 4.9 38.3 1.0
CE A:MET165 5.0 27.3 1.0
H11 A:4WI401 5.0 61.6 1.0

Fluorine binding site 3 out of 6 in 8e1y

Go back to Fluorine Binding Sites List in 8e1y
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193S 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 A193S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:87.5
occ:1.00
 F3 A:4WI401 0.0 87.5 1.0
C22 A:4WI401 1.3 85.1 1.0
F2 A:4WI401 2.1 89.3 1.0
F1 A:4WI401 2.1 81.9 1.0
C21 A:4WI401 2.4 81.1 1.0
HA A:LEU167 2.5 32.2 1.0
H16 A:4WI401 2.5 75.1 1.0
HD3 A:PRO168 2.6 38.3 1.0
N4 A:4WI401 2.7 74.6 1.0
HD23 A:LEU167 3.0 31.6 1.0
O A:GLU166 3.1 30.1 1.0
CA A:LEU167 3.4 32.1 1.0
O4 A:4WI401 3.4 82.6 1.0
CD A:PRO168 3.5 38.8 1.0
HE1 A:MET165 3.5 27.3 1.0
HG3 A:PRO168 3.6 38.3 1.0
H29 A:4WI401 3.6 71.5 1.0
HE2 A:MET165 3.6 27.2 1.0
HE3 A:MET165 3.6 27.3 1.0
CE A:MET165 3.8 27.3 1.0
C A:GLU166 3.9 29.1 1.0
N A:PRO168 4.0 37.1 1.0
CD2 A:LEU167 4.0 31.6 1.0
C A:LEU167 4.0 34.1 1.0
H31 A:4WI401 4.0 71.5 1.0
HG3 A:GLN192 4.0 40.9 1.0
CG A:PRO168 4.1 38.5 1.0
N A:LEU167 4.1 30.7 1.0
C14 A:4WI401 4.1 71.4 1.0
C23 A:4WI401 4.2 71.8 1.0
HD2 A:PRO168 4.2 38.3 1.0
HD21 A:LEU167 4.4 31.6 1.0
CB A:LEU167 4.4 31.6 1.0
H15 A:4WI401 4.4 70.9 1.0
HG A:LEU167 4.5 31.7 1.0
H17 A:4WI401 4.5 68.5 1.0
HD22 A:LEU167 4.5 31.6 1.0
HB3 A:LEU167 4.5 31.8 1.0
HG2 A:PRO168 4.6 38.3 1.0
H18 A:4WI401 4.6 68.6 1.0
CG A:LEU167 4.6 31.6 1.0
C15 A:4WI401 4.6 71.3 1.0
O A:GLN192 4.7 42.8 1.0
H A:GLN192 4.7 45.5 1.0
HE22 A:GLN192 4.7 39.3 1.0
C16 A:4WI401 4.8 67.7 1.0
HG2 A:GLN192 4.9 40.9 1.0
CG A:GLN192 4.9 41.0 1.0
HA A:PRO168 4.9 36.6 1.0
H A:LEU167 4.9 30.6 1.0
HB2 A:MET165 5.0 24.8 1.0
O A:LEU167 5.0 35.4 1.0
CA A:PRO168 5.0 36.2 1.0

Fluorine binding site 4 out of 6 in 8e1y

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Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193S 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 A193S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:93.1
occ:1.00
 F1 B:4WI402 0.0 93.1 1.0
C22 B:4WI402 1.3 93.6 1.0
F3 B:4WI402 2.1 92.9 1.0
F2 B:4WI402 2.1 92.1 1.0
C21 B:4WI402 2.4 91.0 1.0
H16 B:4WI402 2.7 88.0 1.0
N4 B:4WI402 2.7 88.9 1.0
HD3 B:PRO168 3.0 38.4 1.0
O B:GLU166 3.2 30.4 1.0
H29 B:4WI402 3.3 82.6 1.0
O4 B:4WI402 3.4 86.6 1.0
HG3 B:PRO168 3.5 39.1 1.0
HA B:LEU167 3.5 33.4 1.0
H30 B:4WI402 3.5 82.8 1.0
CD B:PRO168 3.8 38.7 1.0
C23 B:4WI402 3.8 82.7 1.0
H19 B:4WI402 3.8 83.0 1.0
C14 B:4WI402 3.9 83.9 1.0
H17 B:4WI402 3.9 83.0 1.0
H15 B:4WI402 4.1 83.2 1.0
CG B:PRO168 4.1 39.4 1.0
N B:PRO168 4.1 36.7 1.0
C16 B:4WI402 4.1 82.8 1.0
HD23 B:LEU167 4.2 32.3 1.0
C15 B:4WI402 4.2 84.1 1.0
CA B:LEU167 4.3 33.5 1.0
C B:GLU166 4.4 32.0 1.0
C B:LEU167 4.4 35.1 1.0
HA B:PRO168 4.5 37.8 1.0
HD2 B:PRO168 4.6 38.4 1.0
HE2 B:MET165 4.6 41.5 1.0
H B:GLN192 4.6 46.0 1.0
H31 B:4WI402 4.7 82.7 1.0
HG2 B:PRO168 4.7 39.1 1.0
HE3 B:MET165 4.8 41.5 1.0
N B:LEU167 4.8 32.3 1.0
CA B:PRO168 4.8 37.6 1.0

Fluorine binding site 5 out of 6 in 8e1y

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Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193S 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 A193S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:92.1
occ:1.00
 F2 B:4WI402 0.0 92.1 1.0
C22 B:4WI402 1.3 93.6 1.0
F3 B:4WI402 2.1 92.9 1.0
F1 B:4WI402 2.1 93.1 1.0
C21 B:4WI402 2.4 91.0 1.0
O4 B:4WI402 2.7 86.6 1.0
O B:THR190 3.2 67.2 1.0
H B:GLN192 3.4 46.0 1.0
N4 B:4WI402 3.5 88.9 1.0
H16 B:4WI402 3.9 88.0 1.0
HE22 B:GLN192 3.9 38.3 1.0
HD3 B:PRO168 3.9 38.4 1.0
HA B:ALA191 3.9 54.9 1.0
HB2 B:GLN192 3.9 40.8 1.0
HG3 B:GLN192 4.0 39.6 1.0
HE2 B:MET165 4.0 41.5 1.0
N B:GLN192 4.1 45.7 1.0
HE3 B:MET165 4.1 41.5 1.0
HE1 B:MET165 4.2 41.5 1.0
O B:GLN189 4.2 81.7 1.0
HA B:GLN189 4.2 79.4 1.0
C B:THR190 4.3 65.0 1.0
CE B:MET165 4.3 41.8 1.0
HD23 B:LEU167 4.4 32.3 1.0
HG3 B:PRO168 4.4 39.1 1.0
H15 B:4WI402 4.5 83.2 1.0
C B:GLN189 4.5 81.6 1.0
NE2 B:GLN192 4.6 38.5 1.0
H17 B:4WI402 4.6 83.0 1.0
CB B:GLN192 4.6 40.8 1.0
C14 B:4WI402 4.6 83.9 1.0
HA B:LEU167 4.7 33.4 1.0
CG B:GLN192 4.7 39.8 1.0
CA B:ALA191 4.7 55.0 1.0
O B:GLN192 4.7 37.1 1.0
O B:GLU166 4.8 30.4 1.0
CD B:PRO168 4.8 38.7 1.0
C B:ALA191 4.8 51.2 1.0
CA B:GLN192 4.9 41.7 1.0
CA B:GLN189 4.9 79.8 1.0
O B:ARG188 4.9 69.1 1.0
N B:ALA191 4.9 59.6 1.0
N B:THR190 5.0 77.2 1.0

Fluorine binding site 6 out of 6 in 8e1y

Go back to Fluorine Binding Sites List in 8e1y
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease A193S 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 A193S Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:92.9
occ:1.00
 F3 B:4WI402 0.0 92.9 1.0
C22 B:4WI402 1.3 93.6 1.0
F2 B:4WI402 2.1 92.1 1.0
F1 B:4WI402 2.1 93.1 1.0
C21 B:4WI402 2.4 91.0 1.0
HD23 B:LEU167 2.4 32.3 1.0
HE2 B:MET165 2.6 41.5 1.0
HA B:LEU167 2.8 33.4 1.0
HD3 B:PRO168 2.9 38.4 1.0
H16 B:4WI402 2.9 88.0 1.0
N4 B:4WI402 3.1 88.9 1.0
O4 B:4WI402 3.2 86.6 1.0
O B:GLU166 3.2 30.4 1.0
HE3 B:MET165 3.3 41.5 1.0
CD2 B:LEU167 3.3 32.4 1.0
CE B:MET165 3.3 41.8 1.0
HB2 B:GLN192 3.4 40.8 1.0
HE1 B:MET165 3.6 41.5 1.0
HD21 B:LEU167 3.6 32.2 1.0
HD22 B:LEU167 3.7 32.2 1.0
CA B:LEU167 3.8 33.5 1.0
CD B:PRO168 3.8 38.7 1.0
C B:GLU166 4.0 32.0 1.0
H B:GLN192 4.0 46.0 1.0
HD2 B:PRO168 4.2 38.4 1.0
N B:LEU167 4.3 32.3 1.0
HE22 B:GLN192 4.3 38.3 1.0
H29 B:4WI402 4.3 82.6 1.0
HB2 B:MET165 4.3 35.3 1.0
CB B:GLN192 4.3 40.8 1.0
O B:GLN192 4.3 37.1 1.0
CG B:LEU167 4.4 31.9 1.0
HG3 B:PRO168 4.4 39.1 1.0
HG B:LEU167 4.4 32.0 1.0
HG3 B:MET165 4.5 37.8 1.0
N B:PRO168 4.5 36.7 1.0
C14 B:4WI402 4.5 83.9 1.0
CB B:LEU167 4.5 32.5 1.0
HG3 B:GLN192 4.6 39.6 1.0
C B:LEU167 4.6 35.1 1.0
CG B:PRO168 4.7 39.4 1.0
NE2 B:GLN192 4.7 38.5 1.0
HB3 B:LEU167 4.7 32.6 1.0
N B:GLN192 4.7 45.7 1.0
H15 B:4WI402 4.8 83.2 1.0
O B:THR190 4.8 67.2 1.0
CG B:GLN192 4.9 39.8 1.0
C B:GLN192 4.9 39.1 1.0
CA B:GLN192 4.9 41.7 1.0
SD B:MET165 4.9 40.6 1.0
HB3 B:GLN192 4.9 40.8 1.0
CD B:GLN192 5.0 37.8 1.0

Reference:

G.D.Noske, G.Oliva, A.S.Godoy. Crystal Structure of Sars-Cov-2 Main Protease A193S Mutant in Complex with Nirmatrelvir To Be Published.
Page generated: Fri Aug 2 17:42:47 2024

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