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Fluorine in PDB 8dz6: Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K in Complex with Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K in Complex with Nirmatrelvir, PDB code: 8dz6 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) 72.52 / 2.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.782, 101.572, 103.561, 90, 90, 90
R / Rfree (%) 22.9 / 29.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K in Complex with Nirmatrelvir (pdb code 8dz6). 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 Mutant Q189K in Complex with Nirmatrelvir, PDB code: 8dz6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8dz6

Go back to Fluorine Binding Sites List in 8dz6
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K 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 Mutant Q189K in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:61.5
occ:1.00
 F1 A:4WI401 0.0 61.5 1.0
C22 A:4WI401 1.3 61.8 1.0
F3 A:4WI401 2.1 62.7 1.0
F2 A:4WI401 2.1 59.0 1.0
C21 A:4WI401 2.4 61.2 1.0
O4 A:4WI401 2.6 65.7 1.0
O A:THR190 3.0 44.8 1.0
H A:THR190 3.1 44.0 1.0
HE22 A:GLN192 3.2 38.1 1.0
HA A:LYS189 3.3 40.5 1.0
HG2 A:GLN192 3.3 40.5 1.0
O A:HOH522 3.4 34.7 1.0
HG3 A:GLN192 3.5 40.5 1.0
N4 A:4WI401 3.6 59.0 1.0
N A:THR190 3.8 43.6 1.0
H16 A:4WI401 3.8 59.3 1.0
CG A:GLN192 3.9 40.8 1.0
HG3 A:LYS189 4.0 44.3 1.0
NE2 A:GLN192 4.0 37.9 1.0
H A:GLN192 4.1 45.8 1.0
HD23 A:LEU167 4.1 35.0 1.0
O A:ARG188 4.1 34.1 1.0
C A:THR190 4.2 46.0 1.0
CA A:LYS189 4.2 40.4 1.0
HD3 A:PRO168 4.3 36.8 1.0
C A:LYS189 4.4 43.7 1.0
CD A:GLN192 4.5 38.5 1.0
HA A:LEU167 4.5 34.1 1.0
H29 A:4WI401 4.6 60.3 1.0
O A:GLN192 4.6 42.6 1.0
CA A:THR190 4.7 45.5 1.0
HE21 A:GLN192 4.7 38.0 1.0
H28 A:4WI401 4.7 50.8 1.0
H15 A:4WI401 4.7 58.5 1.0
HG21 A:THR190 4.7 47.2 1.0
CG A:LYS189 4.8 44.3 1.0
C14 A:4WI401 4.8 58.9 1.0
N A:GLN192 4.8 46.0 1.0
H11 A:4WI401 4.8 53.6 1.0
O A:GLU166 4.8 31.1 1.0
HG2 A:LYS189 4.8 44.2 1.0
HG3 A:PRO168 4.8 36.6 1.0
C A:ARG188 5.0 34.2 1.0

Fluorine binding site 2 out of 6 in 8dz6

Go back to Fluorine Binding Sites List in 8dz6
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K 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 Mutant Q189K in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:59.0
occ:1.00
 F2 A:4WI401 0.0 59.0 1.0
C22 A:4WI401 1.3 61.8 1.0
F1 A:4WI401 2.1 61.5 1.0
F3 A:4WI401 2.1 62.7 1.0
C21 A:4WI401 2.4 61.2 1.0
H16 A:4WI401 2.6 59.3 1.0
N4 A:4WI401 2.8 59.0 1.0
HD23 A:LEU167 3.2 35.0 1.0
O4 A:4WI401 3.3 65.7 1.0
HB2 A:MET165 3.4 31.8 1.0
HE22 A:GLN192 3.4 38.1 1.0
O A:GLU166 3.5 31.1 1.0
HA A:LEU167 3.6 34.1 1.0
SD A:MET165 3.8 38.4 1.0
HG3 A:GLN192 3.8 40.5 1.0
H28 A:4WI401 3.9 50.8 1.0
H26 A:4WI401 3.9 50.7 1.0
NE2 A:GLN192 4.0 37.9 1.0
HG3 A:MET165 4.1 34.1 1.0
CD2 A:LEU167 4.1 35.2 1.0
HD22 A:LEU167 4.2 35.0 1.0
C14 A:4WI401 4.2 58.9 1.0
CB A:MET165 4.2 32.0 1.0
C A:GLU166 4.3 31.8 1.0
HA A:LYS189 4.3 40.5 1.0
CG A:MET165 4.3 33.3 1.0
HG2 A:GLN192 4.3 40.5 1.0
H29 A:4WI401 4.3 60.3 1.0
C20 A:4WI401 4.3 50.5 1.0
HE3 A:MET165 4.4 37.9 1.0
CG A:GLN192 4.4 40.8 1.0
HE21 A:GLN192 4.4 38.0 1.0
H15 A:4WI401 4.5 58.5 1.0
H11 A:4WI401 4.5 53.6 1.0
O A:ARG188 4.5 34.1 1.0
CD A:GLN192 4.5 38.5 1.0
HD3 A:PRO168 4.5 36.8 1.0
HG A:LEU167 4.5 34.5 1.0
CA A:LEU167 4.5 34.2 1.0
HB3 A:MET165 4.6 31.9 1.0
C13 A:4WI401 4.6 55.9 1.0
H A:THR190 4.6 44.0 1.0
CE A:MET165 4.6 37.8 1.0
H27 A:4WI401 4.6 50.8 1.0
N A:LEU167 4.7 32.7 1.0
HD21 A:LEU167 4.8 35.0 1.0
CG A:LEU167 4.8 34.3 1.0
HE1 A:MET165 4.8 37.9 1.0
H A:GLU166 4.9 30.3 1.0
O A:THR190 4.9 44.8 1.0
N3 A:4WI401 5.0 54.0 1.0

Fluorine binding site 3 out of 6 in 8dz6

Go back to Fluorine Binding Sites List in 8dz6
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K 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 Mutant Q189K in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:62.7
occ:1.00
 F3 A:4WI401 0.0 62.7 1.0
C22 A:4WI401 1.3 61.8 1.0
F1 A:4WI401 2.1 61.5 1.0
F2 A:4WI401 2.1 59.0 1.0
C21 A:4WI401 2.4 61.2 1.0
HA A:LEU167 2.5 34.1 1.0
HD3 A:PRO168 2.7 36.8 1.0
H16 A:4WI401 2.8 59.3 1.0
N4 A:4WI401 3.0 59.0 1.0
HD23 A:LEU167 3.0 35.0 1.0
O A:GLU166 3.1 31.1 1.0
O4 A:4WI401 3.2 65.7 1.0
H29 A:4WI401 3.3 60.3 1.0
CA A:LEU167 3.4 34.2 1.0
CD A:PRO168 3.5 37.0 1.0
HG3 A:PRO168 3.6 36.6 1.0
CD2 A:LEU167 3.9 35.2 1.0
N A:PRO168 3.9 36.3 1.0
HG3 A:GLN192 4.0 40.5 1.0
C A:GLU166 4.0 31.8 1.0
C A:LEU167 4.0 35.7 1.0
CG A:PRO168 4.1 36.7 1.0
N A:LEU167 4.1 32.7 1.0
O A:GLN192 4.2 42.6 1.0
C23 A:4WI401 4.2 60.7 1.0
HD2 A:PRO168 4.3 36.8 1.0
O A:HOH522 4.3 34.7 1.0
HD21 A:LEU167 4.3 35.0 1.0
C14 A:4WI401 4.4 58.9 1.0
CB A:LEU167 4.4 33.5 1.0
HD22 A:LEU167 4.5 35.0 1.0
HB3 A:LEU167 4.5 33.8 1.0
HG2 A:GLN192 4.6 40.5 1.0
H30 A:4WI401 4.6 60.4 1.0
HG A:LEU167 4.6 34.5 1.0
CG A:LEU167 4.6 34.3 1.0
HG2 A:PRO168 4.6 36.6 1.0
O A:THR190 4.6 44.8 1.0
H15 A:4WI401 4.7 58.5 1.0
H31 A:4WI401 4.7 60.4 1.0
H A:GLN192 4.7 45.8 1.0
CG A:GLN192 4.7 40.8 1.0
HE22 A:GLN192 4.7 38.1 1.0
HA A:PRO168 4.9 35.8 1.0
C15 A:4WI401 5.0 60.3 1.0
CA A:PRO168 5.0 35.8 1.0
H A:LEU167 5.0 32.9 1.0
O A:LEU167 5.0 39.4 1.0

Fluorine binding site 4 out of 6 in 8dz6

Go back to Fluorine Binding Sites List in 8dz6
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K 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 Mutant Q189K in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:55.3
occ:1.00
 F1 B:4WI401 0.0 55.3 1.0
C22 B:4WI401 1.3 54.8 1.0
F3 B:4WI401 2.1 57.5 1.0
F2 B:4WI401 2.1 54.9 1.0
C21 B:4WI401 2.4 52.4 1.0
H16 B:4WI401 2.6 51.1 1.0
HD3 B:PRO168 2.7 36.2 1.0
N4 B:4WI401 2.8 51.1 1.0
HA B:LEU167 2.8 31.3 1.0
O B:GLU166 3.1 32.4 1.0
HD23 B:LEU167 3.3 27.6 1.0
O4 B:4WI401 3.4 50.6 1.0
CD B:PRO168 3.5 36.4 1.0
HD2 B:PRO168 3.6 36.2 1.0
H17 B:4WI401 3.6 50.3 1.0
CA B:LEU167 3.8 31.3 1.0
H18 B:4WI401 3.9 50.3 1.0
N B:PRO168 4.0 35.8 1.0
C B:GLU166 4.0 31.6 1.0
HB2 B:GLN192 4.1 32.7 1.0
H B:GLN192 4.1 35.8 1.0
C14 B:4WI401 4.1 50.0 1.0
C16 B:4WI401 4.1 50.4 1.0
CD2 B:LEU167 4.2 27.5 1.0
C B:LEU167 4.2 33.9 1.0
H29 B:4WI401 4.3 50.3 1.0
H31 B:4WI401 4.3 50.3 1.0
N B:LEU167 4.4 31.1 1.0
HD21 B:LEU167 4.4 27.6 1.0
H15 B:4WI401 4.4 49.7 1.0
O B:GLN192 4.5 31.4 1.0
C15 B:4WI401 4.5 50.6 1.0
C23 B:4WI401 4.6 50.3 1.0
O B:THR190 4.7 42.3 1.0
HB2 B:MET165 4.8 27.6 1.0
CG B:PRO168 4.8 36.4 1.0
CB B:LEU167 4.8 29.1 1.0
HD22 B:LEU167 4.8 27.6 1.0
HB3 B:LEU167 4.8 29.4 1.0
N B:GLN192 4.9 35.9 1.0
HG3 B:PRO168 4.9 36.2 1.0
HB3 B:PRO168 4.9 35.7 1.0
HA B:PRO168 4.9 35.3 1.0
HG3 B:GLN192 4.9 31.8 1.0
CB B:GLN192 4.9 32.7 1.0
CA B:PRO168 5.0 35.2 1.0

Fluorine binding site 5 out of 6 in 8dz6

Go back to Fluorine Binding Sites List in 8dz6
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K 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 Mutant Q189K in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:54.9
occ:1.00
 F2 B:4WI401 0.0 54.9 1.0
C22 B:4WI401 1.3 54.8 1.0
F1 B:4WI401 2.1 55.3 1.0
F3 B:4WI401 2.1 57.5 1.0
C21 B:4WI401 2.4 52.4 1.0
O4 B:4WI401 2.6 50.6 1.0
O B:THR190 2.8 42.3 1.0
HE22 B:GLN192 3.1 31.1 1.0
HG3 B:GLN192 3.2 31.8 1.0
H B:GLN192 3.4 35.8 1.0
HB2 B:GLN192 3.4 32.7 1.0
N4 B:4WI401 3.6 51.1 1.0
NE2 B:GLN192 3.7 31.3 1.0
O B:LYS189 3.7 54.1 1.0
H16 B:4WI401 3.8 51.1 1.0
CG B:GLN192 3.9 32.0 1.0
N B:GLN192 3.9 35.9 1.0
C B:THR190 3.9 43.0 1.0
CB B:GLN192 4.0 32.7 1.0
HD23 B:LEU167 4.1 27.6 1.0
O B:ARG188 4.1 39.8 1.0
C B:LYS189 4.1 50.5 1.0
HA B:LYS189 4.1 48.9 1.0
HA B:ALA191 4.1 40.6 1.0
CD B:GLN192 4.1 30.5 1.0
HE21 B:GLN192 4.2 31.1 1.0
HD3 B:PRO168 4.2 36.2 1.0
CA B:GLN192 4.6 33.5 1.0
C B:ALA191 4.6 37.9 1.0
HA B:LEU167 4.6 31.3 1.0
H29 B:4WI401 4.7 50.3 1.0
CA B:LYS189 4.7 48.9 1.0
CA B:ALA191 4.7 40.6 1.0
H15 B:4WI401 4.7 49.7 1.0
H25 B:4WI401 4.7 38.4 1.0
N B:THR190 4.7 48.7 1.0
N B:ALA191 4.7 41.9 1.0
O B:GLN192 4.7 31.4 1.0
HG2 B:GLN192 4.8 31.8 1.0
C14 B:4WI401 4.8 50.0 1.0
HB3 B:GLN192 4.9 32.7 1.0
O B:GLU166 4.9 32.4 1.0
CD2 B:LEU167 4.9 27.5 1.0
CA B:THR190 5.0 45.2 1.0
HD21 B:LEU167 5.0 27.6 1.0
HD2 B:PRO168 5.0 36.2 1.0

Fluorine binding site 6 out of 6 in 8dz6

Go back to Fluorine Binding Sites List in 8dz6
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant Q189K 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 Mutant Q189K in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:57.5
occ:1.00
 F3 B:4WI401 0.0 57.5 1.0
C22 B:4WI401 1.3 54.8 1.0
F1 B:4WI401 2.1 55.3 1.0
F2 B:4WI401 2.1 54.9 1.0
C21 B:4WI401 2.4 52.4 1.0
HD23 B:LEU167 2.8 27.6 1.0
H16 B:4WI401 2.9 51.1 1.0
N4 B:4WI401 3.0 51.1 1.0
O4 B:4WI401 3.2 50.6 1.0
HB2 B:MET165 3.4 27.6 1.0
SD B:MET165 3.5 29.9 1.0
HG3 B:MET165 3.5 28.4 1.0
HA B:LEU167 3.5 31.3 1.0
HB2 B:GLN192 3.5 32.7 1.0
O B:GLU166 3.6 32.4 1.0
CD2 B:LEU167 3.7 27.5 1.0
HE22 B:GLN192 3.7 31.1 1.0
HD22 B:LEU167 3.8 27.6 1.0
CG B:MET165 3.9 28.1 1.0
NE2 B:GLN192 3.9 31.3 1.0
HE21 B:GLN192 4.0 31.1 1.0
H23 B:4WI401 4.1 38.4 1.0
HD21 B:LEU167 4.1 27.6 1.0
CB B:MET165 4.1 27.7 1.0
HE3 B:MET165 4.2 28.6 1.0
C B:GLU166 4.3 31.6 1.0
CD B:GLN192 4.3 30.5 1.0
HG3 B:GLN192 4.3 31.8 1.0
HD3 B:PRO168 4.4 36.2 1.0
CA B:LEU167 4.4 31.3 1.0
CB B:GLN192 4.4 32.7 1.0
H25 B:4WI401 4.4 38.4 1.0
CE B:MET165 4.5 28.3 1.0
C14 B:4WI401 4.5 50.0 1.0
HB3 B:MET165 4.5 27.7 1.0
HG B:LEU167 4.6 27.8 1.0
CG B:GLN192 4.6 32.0 1.0
H17 B:4WI401 4.6 50.3 1.0
C19 B:4WI401 4.6 37.8 1.0
N B:LEU167 4.7 31.1 1.0
CG B:LEU167 4.7 28.0 1.0
O B:THR190 4.7 42.3 1.0
H B:GLU166 4.7 30.5 1.0
H15 B:4WI401 4.7 49.7 1.0
HD2 B:PRO168 4.8 36.2 1.0
H24 B:4WI401 4.8 38.4 1.0
H B:GLN192 4.8 35.8 1.0
O B:ARG188 4.8 39.8 1.0
HE1 B:MET165 4.8 28.6 1.0
HG2 B:MET165 4.8 28.4 1.0
N B:GLU166 4.9 30.6 1.0
OE1 B:GLN192 4.9 28.5 1.0
HB3 B:GLN192 4.9 32.7 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 17:41:32 2024

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