Fluorine in PDB 8dz9: Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir
Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir
All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir:
3.4.22.69;
Protein crystallography data
The structure of Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir, PDB code: 8dz9
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)
|
101.53 /
1.66
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.686,
102.808,
101.554,
90,
91.29,
90
|
|
R / Rfree (%)
|
20.8 /
25.1
|
Fluorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir
(pdb code 8dz9). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the
Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir, PDB code: 8dz9:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 1 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:24.4
occ:1.00
|
F1
|
A:4WI401
|
0.0
|
24.4
|
1.0
|
|
C22
|
A:4WI401
|
1.3
|
24.6
|
1.0
|
|
F3
|
A:4WI401
|
2.1
|
25.5
|
1.0
|
|
F2
|
A:4WI401
|
2.1
|
23.9
|
1.0
|
|
HE3
|
A:MET165
|
2.3
|
17.2
|
1.0
|
|
C21
|
A:4WI401
|
2.4
|
23.2
|
1.0
|
|
HD23
|
A:LEU167
|
2.4
|
22.9
|
1.0
|
|
HE2
|
A:MET165
|
2.6
|
17.2
|
1.0
|
|
H16
|
A:4WI401
|
2.8
|
21.6
|
1.0
|
|
CE
|
A:MET165
|
2.9
|
17.2
|
1.0
|
|
N4
|
A:4WI401
|
2.9
|
21.6
|
1.0
|
|
O
|
A:GLU166
|
3.1
|
17.3
|
1.0
|
|
HA
|
A:LEU167
|
3.1
|
19.6
|
1.0
|
|
HE1
|
A:MET165
|
3.2
|
17.2
|
1.0
|
|
O4
|
A:4WI401
|
3.2
|
23.2
|
1.0
|
|
CD2
|
A:LEU167
|
3.3
|
23.5
|
1.0
|
|
HD21
|
A:LEU167
|
3.3
|
22.9
|
1.0
|
|
HB2
|
A:MET165
|
3.4
|
14.2
|
1.0
|
|
HD22
|
A:LEU167
|
3.7
|
22.9
|
1.0
|
|
HB2
|
A:GLN192
|
3.8
|
18.8
|
1.0
|
|
HE22
|
A:GLN192
|
3.8
|
17.8
|
1.0
|
|
C
|
A:GLU166
|
3.9
|
19.0
|
1.0
|
|
CA
|
A:LEU167
|
4.0
|
19.4
|
1.0
|
|
O
|
A:HOH706
|
4.1
|
24.7
|
1.0
|
|
HG3
|
A:MET165
|
4.1
|
15.1
|
1.0
|
|
NE2
|
A:GLN192
|
4.1
|
17.8
|
1.0
|
|
N
|
A:LEU167
|
4.3
|
19.2
|
1.0
|
|
C14
|
A:4WI401
|
4.3
|
20.0
|
1.0
|
|
CB
|
A:MET165
|
4.3
|
14.3
|
1.0
|
|
HE21
|
A:GLN192
|
4.4
|
17.8
|
1.0
|
|
CG
|
A:LEU167
|
4.4
|
21.7
|
1.0
|
|
SD
|
A:MET165
|
4.4
|
17.0
|
1.0
|
|
CG
|
A:MET165
|
4.5
|
14.8
|
1.0
|
|
HD3
|
A:PRO168
|
4.5
|
18.2
|
1.0
|
|
H
|
A:GLU166
|
4.6
|
14.7
|
1.0
|
|
H15
|
A:4WI401
|
4.6
|
19.9
|
1.0
|
|
C13
|
A:4WI401
|
4.6
|
18.4
|
1.0
|
|
CB
|
A:LEU167
|
4.7
|
20.4
|
1.0
|
|
HG
|
A:LEU167
|
4.7
|
22.0
|
1.0
|
|
CD
|
A:GLN192
|
4.7
|
17.6
|
1.0
|
|
H26
|
A:4WI401
|
4.7
|
18.2
|
1.0
|
|
CB
|
A:GLN192
|
4.7
|
18.7
|
1.0
|
|
HB3
|
A:MET165
|
4.7
|
14.1
|
1.0
|
|
N
|
A:GLU166
|
4.8
|
14.5
|
1.0
|
|
HB3
|
A:LEU167
|
4.8
|
20.4
|
1.0
|
|
O3
|
A:4WI401
|
4.8
|
17.5
|
1.0
|
|
H28
|
A:4WI401
|
4.9
|
18.2
|
1.0
|
|
HG3
|
A:GLN192
|
4.9
|
18.2
|
1.0
|
|
H17
|
A:4WI401
|
4.9
|
20.1
|
1.0
|
|
H
|
A:GLN192
|
5.0
|
19.7
|
1.0
|
|
O
|
A:THR190
|
5.0
|
20.9
|
1.0
|
|
H29
|
A:4WI401
|
5.0
|
19.6
|
1.0
|
|
Fluorine binding site 2 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 2 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:23.9
occ:1.00
|
F2
|
A:4WI401
|
0.0
|
23.9
|
1.0
|
|
C22
|
A:4WI401
|
1.3
|
24.6
|
1.0
|
|
O
|
A:HOH706
|
2.1
|
24.7
|
1.0
|
|
F1
|
A:4WI401
|
2.1
|
24.4
|
1.0
|
|
F3
|
A:4WI401
|
2.2
|
25.5
|
1.0
|
|
C21
|
A:4WI401
|
2.4
|
23.2
|
1.0
|
|
H16
|
A:4WI401
|
2.7
|
21.6
|
1.0
|
|
HA
|
A:LEU167
|
2.9
|
19.6
|
1.0
|
|
N4
|
A:4WI401
|
2.9
|
21.6
|
1.0
|
|
O
|
A:GLU166
|
3.3
|
17.3
|
1.0
|
|
O4
|
A:4WI401
|
3.3
|
23.2
|
1.0
|
|
HD3
|
A:PRO168
|
3.5
|
18.2
|
1.0
|
|
HG3
|
A:PRO168
|
3.6
|
18.5
|
1.0
|
|
O
|
A:HOH711
|
3.7
|
34.4
|
1.0
|
|
HD23
|
A:LEU167
|
3.7
|
22.9
|
1.0
|
|
CA
|
A:LEU167
|
3.8
|
19.4
|
1.0
|
|
H29
|
A:4WI401
|
3.9
|
19.6
|
1.0
|
|
CD
|
A:PRO168
|
4.2
|
18.1
|
1.0
|
|
H
|
A:GLN192
|
4.2
|
19.7
|
1.0
|
|
C
|
A:GLU166
|
4.2
|
19.0
|
1.0
|
|
HB2
|
A:GLN192
|
4.3
|
18.8
|
1.0
|
|
HD21
|
A:LEU167
|
4.3
|
22.9
|
1.0
|
|
O
|
A:GLN192
|
4.3
|
19.0
|
1.0
|
|
C14
|
A:4WI401
|
4.3
|
20.0
|
1.0
|
|
O
|
A:HOH697
|
4.3
|
23.1
|
1.0
|
|
CG
|
A:PRO168
|
4.3
|
18.5
|
1.0
|
|
C
|
A:LEU167
|
4.3
|
19.6
|
1.0
|
|
N
|
A:PRO168
|
4.3
|
18.1
|
1.0
|
|
HE3
|
A:MET165
|
4.4
|
17.2
|
1.0
|
|
CD2
|
A:LEU167
|
4.4
|
23.5
|
1.0
|
|
H31
|
A:4WI401
|
4.5
|
19.6
|
1.0
|
|
N
|
A:LEU167
|
4.5
|
19.2
|
1.0
|
|
C23
|
A:4WI401
|
4.6
|
19.6
|
1.0
|
|
H15
|
A:4WI401
|
4.6
|
19.9
|
1.0
|
|
HE2
|
A:MET165
|
4.6
|
17.2
|
1.0
|
|
HB3
|
A:LEU167
|
4.7
|
20.4
|
1.0
|
|
H17
|
A:4WI401
|
4.7
|
20.1
|
1.0
|
|
CB
|
A:LEU167
|
4.8
|
20.4
|
1.0
|
|
O
|
A:THR190
|
4.8
|
20.9
|
1.0
|
|
H18
|
A:4WI401
|
4.9
|
20.1
|
1.0
|
|
C15
|
A:4WI401
|
4.9
|
19.6
|
1.0
|
|
HE22
|
A:GLN192
|
4.9
|
17.8
|
1.0
|
|
HG2
|
A:PRO168
|
4.9
|
18.5
|
1.0
|
|
CE
|
A:MET165
|
4.9
|
17.2
|
1.0
|
|
Fluorine binding site 3 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 3 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:25.5
occ:1.00
|
F3
|
A:4WI401
|
0.0
|
25.5
|
1.0
|
|
C22
|
A:4WI401
|
1.3
|
24.6
|
1.0
|
|
F1
|
A:4WI401
|
2.1
|
24.4
|
1.0
|
|
F2
|
A:4WI401
|
2.2
|
23.9
|
1.0
|
|
C21
|
A:4WI401
|
2.4
|
23.2
|
1.0
|
|
O4
|
A:4WI401
|
2.6
|
23.2
|
1.0
|
|
HE22
|
A:GLN192
|
2.9
|
17.8
|
1.0
|
|
O
|
A:THR190
|
3.0
|
20.9
|
1.0
|
|
O
|
A:HOH706
|
3.2
|
24.7
|
1.0
|
|
HB2
|
A:GLN192
|
3.5
|
18.8
|
1.0
|
|
HE3
|
A:MET165
|
3.5
|
17.2
|
1.0
|
|
H
|
A:GLN192
|
3.6
|
19.7
|
1.0
|
|
N4
|
A:4WI401
|
3.6
|
21.6
|
1.0
|
|
HG3
|
A:GLN192
|
3.6
|
18.2
|
1.0
|
|
NE2
|
A:GLN192
|
3.6
|
17.8
|
1.0
|
|
HA
|
A:GLN189
|
3.7
|
21.5
|
1.0
|
|
H16
|
A:4WI401
|
3.8
|
21.6
|
1.0
|
|
HE1
|
A:MET165
|
3.8
|
17.2
|
1.0
|
|
O
|
A:HOH697
|
4.0
|
23.1
|
1.0
|
|
CE
|
A:MET165
|
4.0
|
17.2
|
1.0
|
|
HE2
|
A:MET165
|
4.0
|
17.2
|
1.0
|
|
O
|
A:ARG188
|
4.1
|
17.6
|
1.0
|
|
HE21
|
A:GLN192
|
4.1
|
17.8
|
1.0
|
|
CG
|
A:GLN192
|
4.1
|
18.3
|
1.0
|
|
CB
|
A:GLN192
|
4.2
|
18.7
|
1.0
|
|
N
|
A:GLN192
|
4.2
|
19.8
|
1.0
|
|
C
|
A:THR190
|
4.2
|
20.9
|
1.0
|
|
CD
|
A:GLN192
|
4.3
|
17.6
|
1.0
|
|
HD23
|
A:LEU167
|
4.3
|
22.9
|
1.0
|
|
HA
|
A:LEU167
|
4.5
|
19.6
|
1.0
|
|
CA
|
A:GLN189
|
4.5
|
21.6
|
1.0
|
|
HD21
|
A:LEU167
|
4.5
|
22.9
|
1.0
|
|
H
|
A:THR190
|
4.6
|
22.9
|
1.0
|
|
N
|
A:THR190
|
4.6
|
23.8
|
1.0
|
|
C
|
A:GLN189
|
4.6
|
22.3
|
1.0
|
|
O
|
A:GLN192
|
4.7
|
19.0
|
1.0
|
|
CA
|
A:GLN192
|
4.7
|
19.7
|
1.0
|
|
HA
|
A:ALA191
|
4.7
|
20.8
|
1.0
|
|
H15
|
A:4WI401
|
4.7
|
19.9
|
1.0
|
|
H29
|
A:4WI401
|
4.7
|
19.6
|
1.0
|
|
C14
|
A:4WI401
|
4.8
|
20.0
|
1.0
|
|
HG2
|
A:GLN189
|
4.8
|
24.1
|
1.0
|
|
O
|
A:GLU166
|
4.8
|
17.3
|
1.0
|
|
CD2
|
A:LEU167
|
4.9
|
23.5
|
1.0
|
|
HD3
|
A:PRO168
|
4.9
|
18.2
|
1.0
|
|
C
|
A:ALA191
|
4.9
|
19.3
|
1.0
|
|
HB3
|
A:GLN192
|
5.0
|
18.8
|
1.0
|
|
Fluorine binding site 4 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 4 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:23.2
occ:1.00
|
F1
|
B:4WI401
|
0.0
|
23.2
|
1.0
|
|
C22
|
B:4WI401
|
1.3
|
24.9
|
1.0
|
|
F3
|
B:4WI401
|
2.1
|
30.7
|
1.0
|
|
F2
|
B:4WI401
|
2.1
|
26.3
|
1.0
|
|
C21
|
B:4WI401
|
2.4
|
23.3
|
1.0
|
|
HB2
|
B:GLN192
|
2.7
|
19.0
|
1.0
|
|
O4
|
B:4WI401
|
2.7
|
23.9
|
1.0
|
|
HG3
|
B:GLN192
|
2.7
|
18.4
|
1.0
|
|
HE22
|
B:GLN192
|
2.9
|
17.5
|
1.0
|
|
O
|
B:THR190
|
2.9
|
26.4
|
1.0
|
|
CG
|
B:GLN192
|
3.3
|
18.8
|
1.0
|
|
NE2
|
B:GLN192
|
3.3
|
17.7
|
1.0
|
|
CB
|
B:GLN192
|
3.4
|
18.5
|
1.0
|
|
H
|
B:GLN192
|
3.4
|
21.4
|
1.0
|
|
HE3
|
B:MET165
|
3.4
|
20.2
|
1.0
|
|
CD
|
B:GLN192
|
3.5
|
17.2
|
1.0
|
|
N4
|
B:4WI401
|
3.6
|
20.4
|
1.0
|
|
H
|
B:THR190
|
3.8
|
23.0
|
1.0
|
|
H16
|
B:4WI401
|
3.8
|
21.1
|
1.0
|
|
N
|
B:GLN192
|
3.8
|
21.2
|
1.0
|
|
HE21
|
B:GLN192
|
3.9
|
17.5
|
1.0
|
|
CA
|
B:GLN192
|
4.1
|
20.4
|
1.0
|
|
HB3
|
B:GLN192
|
4.1
|
19.0
|
1.0
|
|
C
|
B:THR190
|
4.2
|
24.5
|
1.0
|
|
HG2
|
B:GLN192
|
4.2
|
18.3
|
1.0
|
|
CE
|
B:MET165
|
4.2
|
19.7
|
1.0
|
|
HE1
|
B:MET165
|
4.2
|
20.2
|
1.0
|
|
HA
|
B:LEU167
|
4.4
|
19.1
|
1.0
|
|
O
|
B:GLN192
|
4.4
|
21.6
|
1.0
|
|
HA
|
B:GLN189
|
4.4
|
21.4
|
1.0
|
|
O
|
B:ARG188
|
4.4
|
18.1
|
1.0
|
|
HD3
|
B:PRO168
|
4.4
|
19.3
|
1.0
|
|
N
|
B:THR190
|
4.5
|
23.1
|
1.0
|
|
OE1
|
B:GLN192
|
4.5
|
16.7
|
1.0
|
|
O
|
B:GLU166
|
4.6
|
16.8
|
1.0
|
|
C
|
B:ALA191
|
4.6
|
22.7
|
1.0
|
|
C
|
B:GLN192
|
4.7
|
19.2
|
1.0
|
|
HG
|
B:LEU167
|
4.7
|
19.5
|
1.0
|
|
HA
|
B:ALA191
|
4.7
|
24.3
|
1.0
|
|
HD11
|
B:LEU167
|
4.8
|
19.5
|
1.0
|
|
H15
|
B:4WI401
|
4.8
|
20.5
|
1.0
|
|
C14
|
B:4WI401
|
4.9
|
20.6
|
1.0
|
|
HB2
|
B:MET165
|
4.9
|
15.9
|
1.0
|
|
HG21
|
B:THR190
|
4.9
|
25.0
|
1.0
|
|
HA
|
B:GLN192
|
5.0
|
20.0
|
1.0
|
|
HE2
|
B:MET165
|
5.0
|
20.2
|
1.0
|
|
SD
|
B:MET165
|
5.0
|
21.8
|
1.0
|
|
Fluorine binding site 5 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 5 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:26.3
occ:1.00
|
F2
|
B:4WI401
|
0.0
|
26.3
|
1.0
|
|
C22
|
B:4WI401
|
1.3
|
24.9
|
1.0
|
|
F3
|
B:4WI401
|
2.1
|
30.7
|
1.0
|
|
F1
|
B:4WI401
|
2.1
|
23.2
|
1.0
|
|
C21
|
B:4WI401
|
2.3
|
23.3
|
1.0
|
|
HE3
|
B:MET165
|
2.5
|
20.2
|
1.0
|
|
H16
|
B:4WI401
|
2.6
|
21.1
|
1.0
|
|
N4
|
B:4WI401
|
2.8
|
20.4
|
1.0
|
|
O
|
B:GLU166
|
2.9
|
16.8
|
1.0
|
|
HB2
|
B:MET165
|
3.0
|
15.9
|
1.0
|
|
HD11
|
B:LEU167
|
3.1
|
19.5
|
1.0
|
|
O4
|
B:4WI401
|
3.3
|
23.9
|
1.0
|
|
HA
|
B:LEU167
|
3.3
|
19.1
|
1.0
|
|
HG3
|
B:MET165
|
3.3
|
17.8
|
1.0
|
|
CE
|
B:MET165
|
3.4
|
19.7
|
1.0
|
|
HB2
|
B:GLN192
|
3.7
|
19.0
|
1.0
|
|
C
|
B:GLU166
|
3.7
|
16.0
|
1.0
|
|
CG
|
B:MET165
|
3.8
|
17.3
|
1.0
|
|
CB
|
B:MET165
|
3.8
|
15.9
|
1.0
|
|
SD
|
B:MET165
|
3.9
|
21.8
|
1.0
|
|
HE1
|
B:MET165
|
3.9
|
20.2
|
1.0
|
|
HG
|
B:LEU167
|
3.9
|
19.5
|
1.0
|
|
CD1
|
B:LEU167
|
3.9
|
19.4
|
1.0
|
|
HE2
|
B:MET165
|
4.0
|
20.2
|
1.0
|
|
H
|
B:GLU166
|
4.0
|
15.3
|
1.0
|
|
HD12
|
B:LEU167
|
4.1
|
19.4
|
1.0
|
|
N
|
B:LEU167
|
4.1
|
17.8
|
1.0
|
|
C14
|
B:4WI401
|
4.1
|
20.6
|
1.0
|
|
CA
|
B:LEU167
|
4.1
|
19.1
|
1.0
|
|
HB3
|
B:MET165
|
4.3
|
15.9
|
1.0
|
|
N
|
B:GLU166
|
4.3
|
15.5
|
1.0
|
|
HE22
|
B:GLN192
|
4.3
|
17.5
|
1.0
|
|
C13
|
B:4WI401
|
4.4
|
20.2
|
1.0
|
|
CG
|
B:LEU167
|
4.4
|
19.7
|
1.0
|
|
NE2
|
B:GLN192
|
4.4
|
17.7
|
1.0
|
|
O3
|
B:4WI401
|
4.5
|
19.6
|
1.0
|
|
H15
|
B:4WI401
|
4.5
|
20.5
|
1.0
|
|
HD3
|
B:PRO168
|
4.5
|
19.3
|
1.0
|
|
CB
|
B:GLN192
|
4.6
|
18.5
|
1.0
|
|
HG3
|
B:GLN192
|
4.6
|
18.4
|
1.0
|
|
H26
|
B:4WI401
|
4.6
|
16.2
|
1.0
|
|
CA
|
B:GLU166
|
4.6
|
16.0
|
1.0
|
|
HE21
|
B:GLN192
|
4.7
|
17.5
|
1.0
|
|
CD
|
B:GLN192
|
4.7
|
17.2
|
1.0
|
|
HD13
|
B:LEU167
|
4.7
|
19.5
|
1.0
|
|
H29
|
B:4WI401
|
4.7
|
20.0
|
1.0
|
|
O
|
B:HOH602
|
4.7
|
18.9
|
1.0
|
|
HG2
|
B:MET165
|
4.7
|
17.8
|
1.0
|
|
CG
|
B:GLN192
|
4.8
|
18.8
|
1.0
|
|
CB
|
B:LEU167
|
4.8
|
19.9
|
1.0
|
|
H
|
B:LEU167
|
4.9
|
17.6
|
1.0
|
|
C
|
B:MET165
|
4.9
|
14.3
|
1.0
|
|
H28
|
B:4WI401
|
4.9
|
16.2
|
1.0
|
|
CA
|
B:MET165
|
5.0
|
14.6
|
1.0
|
|
Fluorine binding site 6 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 6 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:30.7
occ:1.00
|
F3
|
B:4WI401
|
0.0
|
30.7
|
1.0
|
|
C22
|
B:4WI401
|
1.3
|
24.9
|
1.0
|
|
F1
|
B:4WI401
|
2.1
|
23.2
|
1.0
|
|
F2
|
B:4WI401
|
2.1
|
26.3
|
1.0
|
|
C21
|
B:4WI401
|
2.4
|
23.3
|
1.0
|
|
H16
|
B:4WI401
|
2.7
|
21.1
|
1.0
|
|
HA
|
B:LEU167
|
2.8
|
19.1
|
1.0
|
|
HD3
|
B:PRO168
|
2.8
|
19.3
|
1.0
|
|
N4
|
B:4WI401
|
2.9
|
20.4
|
1.0
|
|
O
|
B:GLU166
|
3.1
|
16.8
|
1.0
|
|
O4
|
B:4WI401
|
3.3
|
23.9
|
1.0
|
|
O
|
B:HOH602
|
3.3
|
18.9
|
1.0
|
|
O
|
B:HOH637
|
3.4
|
26.3
|
1.0
|
|
CD
|
B:PRO168
|
3.6
|
19.1
|
1.0
|
|
HB2
|
B:GLN192
|
3.6
|
19.0
|
1.0
|
|
CA
|
B:LEU167
|
3.7
|
19.1
|
1.0
|
|
HD2
|
B:PRO168
|
3.7
|
19.3
|
1.0
|
|
H
|
B:GLN192
|
3.9
|
21.4
|
1.0
|
|
C
|
B:GLU166
|
4.0
|
16.0
|
1.0
|
|
O
|
B:GLN192
|
4.0
|
21.6
|
1.0
|
|
HD11
|
B:LEU167
|
4.1
|
19.5
|
1.0
|
|
HG
|
B:LEU167
|
4.2
|
19.5
|
1.0
|
|
N
|
B:PRO168
|
4.2
|
19.8
|
1.0
|
|
HE3
|
B:MET165
|
4.2
|
20.2
|
1.0
|
|
N
|
B:LEU167
|
4.2
|
17.8
|
1.0
|
|
O
|
B:THR190
|
4.3
|
26.4
|
1.0
|
|
C
|
B:LEU167
|
4.3
|
20.0
|
1.0
|
|
C14
|
B:4WI401
|
4.4
|
20.6
|
1.0
|
|
H17
|
B:4WI401
|
4.4
|
20.8
|
1.0
|
|
HG3
|
B:GLN192
|
4.5
|
18.4
|
1.0
|
|
CB
|
B:GLN192
|
4.5
|
18.5
|
1.0
|
|
N
|
B:GLN192
|
4.6
|
21.2
|
1.0
|
|
H15
|
B:4WI401
|
4.7
|
20.5
|
1.0
|
|
CB
|
B:LEU167
|
4.7
|
19.9
|
1.0
|
|
C
|
B:GLN192
|
4.8
|
19.2
|
1.0
|
|
CG
|
B:LEU167
|
4.8
|
19.7
|
1.0
|
|
H29
|
B:4WI401
|
4.8
|
20.0
|
1.0
|
|
HG3
|
B:PRO168
|
4.8
|
19.0
|
1.0
|
|
CG
|
B:PRO168
|
4.8
|
19.2
|
1.0
|
|
CA
|
B:GLN192
|
4.8
|
20.4
|
1.0
|
|
HB2
|
B:MET165
|
4.8
|
15.9
|
1.0
|
|
HB3
|
B:LEU167
|
4.9
|
19.6
|
1.0
|
|
CD1
|
B:LEU167
|
4.9
|
19.4
|
1.0
|
|
H19
|
B:4WI401
|
4.9
|
20.8
|
1.0
|
|
CG
|
B:GLN192
|
5.0
|
18.8
|
1.0
|
|
HE22
|
B:GLN192
|
5.0
|
17.5
|
1.0
|
|
C16
|
B:4WI401
|
5.0
|
20.8
|
1.0
|
|
Fluorine binding site 7 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 7 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 7 of Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F401
b:32.7
occ:1.00
|
F1
|
C:4WI401
|
0.0
|
32.7
|
1.0
|
|
C22
|
C:4WI401
|
1.3
|
31.7
|
1.0
|
|
F3
|
C:4WI401
|
2.1
|
30.6
|
1.0
|
|
F2
|
C:4WI401
|
2.2
|
35.0
|
1.0
|
|
C21
|
C:4WI401
|
2.3
|
29.4
|
1.0
|
|
H16
|
C:4WI401
|
2.6
|
24.1
|
1.0
|
|
O
|
C:HOH642
|
2.8
|
27.2
|
1.0
|
|
N4
|
C:4WI401
|
2.9
|
24.1
|
1.0
|
|
HA
|
C:LEU167
|
3.0
|
21.8
|
1.0
|
|
O
|
C:HOH522
|
3.1
|
19.4
|
1.0
|
|
O4
|
C:4WI401
|
3.2
|
33.5
|
1.0
|
|
HD23
|
C:LEU167
|
3.3
|
22.0
|
1.0
|
|
O
|
C:GLU166
|
3.4
|
20.8
|
1.0
|
|
O
|
C:HOH650
|
3.5
|
39.0
|
1.0
|
|
HD3
|
C:PRO168
|
3.5
|
19.8
|
1.0
|
|
O
|
C:HOH592
|
3.5
|
16.8
|
1.0
|
|
HG3
|
C:PRO168
|
3.8
|
19.7
|
1.0
|
|
HB2
|
C:GLN192
|
3.9
|
19.4
|
1.0
|
|
CA
|
C:LEU167
|
4.0
|
22.4
|
1.0
|
|
H
|
C:GLN192
|
4.1
|
20.2
|
1.0
|
|
HE2
|
C:MET165
|
4.1
|
22.8
|
1.0
|
|
HE3
|
C:MET165
|
4.2
|
22.8
|
1.0
|
|
C
|
C:GLU166
|
4.3
|
19.6
|
1.0
|
|
CD2
|
C:LEU167
|
4.3
|
22.1
|
1.0
|
|
C14
|
C:4WI401
|
4.3
|
20.2
|
1.0
|
|
CD
|
C:PRO168
|
4.3
|
19.7
|
1.0
|
|
H29
|
C:4WI401
|
4.4
|
18.0
|
1.0
|
|
O
|
C:GLN192
|
4.4
|
22.6
|
1.0
|
|
N
|
C:LEU167
|
4.5
|
21.3
|
1.0
|
|
CG
|
C:PRO168
|
4.5
|
20.0
|
1.0
|
|
C
|
C:LEU167
|
4.5
|
20.9
|
1.0
|
|
CE
|
C:MET165
|
4.6
|
22.2
|
1.0
|
|
H15
|
C:4WI401
|
4.6
|
20.3
|
1.0
|
|
HG
|
C:LEU167
|
4.6
|
22.1
|
1.0
|
|
N
|
C:PRO168
|
4.6
|
20.0
|
1.0
|
|
HD22
|
C:LEU167
|
4.6
|
22.0
|
1.0
|
|
O
|
C:THR190
|
4.7
|
22.4
|
1.0
|
|
HE1
|
C:MET165
|
4.8
|
22.7
|
1.0
|
|
HD21
|
C:LEU167
|
4.8
|
22.0
|
1.0
|
|
CB
|
C:GLN192
|
4.8
|
19.2
|
1.0
|
|
CG
|
C:LEU167
|
4.8
|
21.8
|
1.0
|
|
N
|
C:GLN192
|
4.8
|
19.9
|
1.0
|
|
CB
|
C:LEU167
|
4.9
|
21.9
|
1.0
|
|
H17
|
C:4WI401
|
4.9
|
19.1
|
1.0
|
|
HB3
|
C:LEU167
|
4.9
|
22.0
|
1.0
|
|
HB2
|
C:MET165
|
5.0
|
18.9
|
1.0
|
|
HE22
|
C:GLN192
|
5.0
|
18.3
|
1.0
|
|
Fluorine binding site 8 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 8 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 8 of Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F401
b:35.0
occ:1.00
|
F2
|
C:4WI401
|
0.0
|
35.0
|
1.0
|
|
C22
|
C:4WI401
|
1.3
|
31.7
|
1.0
|
|
F3
|
C:4WI401
|
2.1
|
30.6
|
1.0
|
|
F1
|
C:4WI401
|
2.2
|
32.7
|
1.0
|
|
C21
|
C:4WI401
|
2.3
|
29.4
|
1.0
|
|
N4
|
C:4WI401
|
2.8
|
24.1
|
1.0
|
|
H16
|
C:4WI401
|
2.9
|
24.1
|
1.0
|
|
HA
|
C:GLN189
|
3.0
|
21.2
|
1.0
|
|
O
|
C:HOH650
|
3.2
|
39.0
|
1.0
|
|
O4
|
C:4WI401
|
3.3
|
33.5
|
1.0
|
|
O
|
C:THR190
|
3.5
|
22.4
|
1.0
|
|
HG2
|
C:GLN189
|
3.5
|
21.9
|
1.0
|
|
H15
|
C:4WI401
|
3.6
|
20.3
|
1.0
|
|
O
|
C:HOH642
|
3.7
|
27.2
|
1.0
|
|
H29
|
C:4WI401
|
3.8
|
18.0
|
1.0
|
|
O
|
C:HOH627
|
3.8
|
22.5
|
1.0
|
|
C14
|
C:4WI401
|
3.9
|
20.2
|
1.0
|
|
CA
|
C:GLN189
|
3.9
|
21.4
|
1.0
|
|
O
|
C:HOH522
|
4.0
|
19.4
|
1.0
|
|
H11
|
C:4WI401
|
4.1
|
18.0
|
1.0
|
|
HE22
|
C:GLN189
|
4.2
|
22.4
|
1.0
|
|
C
|
C:GLN189
|
4.2
|
22.2
|
1.0
|
|
HE3
|
C:MET165
|
4.2
|
22.8
|
1.0
|
|
O
|
C:ARG188
|
4.3
|
17.8
|
1.0
|
|
HE22
|
C:GLN192
|
4.3
|
18.3
|
1.0
|
|
CG
|
C:GLN189
|
4.4
|
22.3
|
1.0
|
|
H
|
C:GLN192
|
4.4
|
20.2
|
1.0
|
|
N
|
C:THR190
|
4.5
|
23.0
|
1.0
|
|
C
|
C:THR190
|
4.5
|
21.2
|
1.0
|
|
CB
|
C:GLN189
|
4.5
|
21.4
|
1.0
|
|
HB3
|
C:GLN189
|
4.5
|
21.6
|
1.0
|
|
HB2
|
C:GLN192
|
4.6
|
19.4
|
1.0
|
|
H
|
C:THR190
|
4.6
|
22.7
|
1.0
|
|
C23
|
C:4WI401
|
4.7
|
17.6
|
1.0
|
|
O
|
C:GLN189
|
4.7
|
23.0
|
1.0
|
|
HE1
|
C:MET165
|
4.8
|
22.7
|
1.0
|
|
HE2
|
C:MET165
|
4.8
|
22.8
|
1.0
|
|
CE
|
C:MET165
|
4.8
|
22.2
|
1.0
|
|
C13
|
C:4WI401
|
4.8
|
18.9
|
1.0
|
|
NE2
|
C:GLN189
|
4.8
|
22.8
|
1.0
|
|
HG3
|
C:GLN192
|
4.9
|
19.2
|
1.0
|
|
C15
|
C:4WI401
|
4.9
|
18.9
|
1.0
|
|
HA
|
C:ALA191
|
4.9
|
21.1
|
1.0
|
|
O
|
C:HOH592
|
4.9
|
16.8
|
1.0
|
|
N
|
C:GLN189
|
5.0
|
19.6
|
1.0
|
|
C10
|
C:4WI401
|
5.0
|
18.0
|
1.0
|
|
O
|
C:GLU166
|
5.0
|
20.8
|
1.0
|
|
NE2
|
C:GLN192
|
5.0
|
18.1
|
1.0
|
|
Fluorine binding site 9 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 9 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 9 of Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F401
b:30.6
occ:1.00
|
F3
|
C:4WI401
|
0.0
|
30.6
|
1.0
|
|
C22
|
C:4WI401
|
1.3
|
31.7
|
1.0
|
|
F2
|
C:4WI401
|
2.1
|
35.0
|
1.0
|
|
F1
|
C:4WI401
|
2.1
|
32.7
|
1.0
|
|
C21
|
C:4WI401
|
2.4
|
29.4
|
1.0
|
|
O4
|
C:4WI401
|
2.7
|
33.5
|
1.0
|
|
HE3
|
C:MET165
|
2.7
|
22.8
|
1.0
|
|
HE2
|
C:MET165
|
2.8
|
22.8
|
1.0
|
|
HE1
|
C:MET165
|
2.9
|
22.7
|
1.0
|
|
CE
|
C:MET165
|
3.0
|
22.2
|
1.0
|
|
HE22
|
C:GLN192
|
3.0
|
18.3
|
1.0
|
|
HB2
|
C:GLN192
|
3.1
|
19.4
|
1.0
|
|
NE2
|
C:GLN192
|
3.4
|
18.1
|
1.0
|
|
HD23
|
C:LEU167
|
3.5
|
22.0
|
1.0
|
|
N4
|
C:4WI401
|
3.6
|
24.1
|
1.0
|
|
O
|
C:THR190
|
3.6
|
22.4
|
1.0
|
|
HG3
|
C:GLN192
|
3.8
|
19.2
|
1.0
|
|
HE21
|
C:GLN192
|
3.8
|
18.3
|
1.0
|
|
H16
|
C:4WI401
|
3.8
|
24.1
|
1.0
|
|
O
|
C:ARG188
|
3.9
|
17.8
|
1.0
|
|
CB
|
C:GLN192
|
3.9
|
19.2
|
1.0
|
|
HA
|
C:GLN189
|
3.9
|
21.2
|
1.0
|
|
CD
|
C:GLN192
|
4.0
|
18.6
|
1.0
|
|
CG
|
C:GLN192
|
4.1
|
19.4
|
1.0
|
|
H
|
C:GLN192
|
4.1
|
20.2
|
1.0
|
|
O
|
C:HOH522
|
4.2
|
19.4
|
1.0
|
|
HD22
|
C:LEU167
|
4.2
|
22.0
|
1.0
|
|
CD2
|
C:LEU167
|
4.3
|
22.1
|
1.0
|
|
HA
|
C:LEU167
|
4.4
|
21.8
|
1.0
|
|
HB2
|
C:MET165
|
4.4
|
18.9
|
1.0
|
|
HB3
|
C:GLN192
|
4.5
|
19.4
|
1.0
|
|
N
|
C:GLN192
|
4.6
|
19.9
|
1.0
|
|
O
|
C:HOH650
|
4.6
|
39.0
|
1.0
|
|
O
|
C:GLU166
|
4.7
|
20.8
|
1.0
|
|
H11
|
C:4WI401
|
4.7
|
18.0
|
1.0
|
|
C14
|
C:4WI401
|
4.7
|
20.2
|
1.0
|
|
SD
|
C:MET165
|
4.7
|
24.4
|
1.0
|
|
H
|
C:THR190
|
4.8
|
22.7
|
1.0
|
|
H25
|
C:4WI401
|
4.8
|
18.3
|
1.0
|
|
H15
|
C:4WI401
|
4.8
|
20.3
|
1.0
|
|
CA
|
C:GLN192
|
4.8
|
20.0
|
1.0
|
|
O
|
C:HOH642
|
4.8
|
27.2
|
1.0
|
|
C
|
C:THR190
|
4.8
|
21.2
|
1.0
|
|
OE1
|
C:GLN192
|
4.8
|
19.5
|
1.0
|
|
CA
|
C:GLN189
|
4.9
|
21.4
|
1.0
|
|
HG
|
C:LEU167
|
4.9
|
22.1
|
1.0
|
|
HG2
|
C:GLN189
|
4.9
|
21.9
|
1.0
|
|
HD21
|
C:LEU167
|
4.9
|
22.0
|
1.0
|
|
C
|
C:ARG188
|
5.0
|
17.9
|
1.0
|
|
N
|
C:THR190
|
5.0
|
23.0
|
1.0
|
|
Fluorine binding site 10 out
of 12 in 8dz9
Go back to
Fluorine Binding Sites List in 8dz9
Fluorine binding site 10 out
of 12 in the Crystal Structure of Sars-Cov-2 Main Protease G143S 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 10 of Crystal Structure of Sars-Cov-2 Main Protease G143S Mutant in Complex with Nirmatrelvir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F401
b:25.7
occ:1.00
|
F1
|
D:4WI401
|
0.0
|
25.7
|
1.0
|
|
C22
|
D:4WI401
|
1.3
|
25.0
|
1.0
|
|
F3
|
D:4WI401
|
2.1
|
26.8
|
1.0
|
|
F2
|
D:4WI401
|
2.1
|
30.7
|
1.0
|
|
C21
|
D:4WI401
|
2.4
|
25.0
|
1.0
|
|
HD3
|
D:PRO168
|
2.8
|
19.8
|
1.0
|
|
HD23
|
D:LEU167
|
3.1
|
16.8
|
1.0
|
|
H16
|
D:4WI401
|
3.1
|
23.0
|
1.0
|
|
O4
|
D:4WI401
|
3.1
|
24.0
|
1.0
|
|
N4
|
D:4WI401
|
3.2
|
23.3
|
1.0
|
|
HA
|
D:LEU167
|
3.3
|
17.6
|
1.0
|
|
HB2
|
D:GLN192
|
3.4
|
19.8
|
1.0
|
|
H
|
D:GLN192
|
3.5
|
22.2
|
1.0
|
|
HG3
|
D:PRO168
|
3.6
|
20.1
|
1.0
|
|
O
|
D:GLN192
|
3.6
|
24.7
|
1.0
|
|
CD
|
D:PRO168
|
3.7
|
19.5
|
1.0
|
|
O
|
D:GLU166
|
3.7
|
17.7
|
1.0
|
|
HG3
|
D:GLN192
|
3.9
|
18.4
|
1.0
|
|
CD2
|
D:LEU167
|
4.0
|
16.8
|
1.0
|
|
HE3
|
D:MET165
|
4.0
|
22.6
|
1.0
|
|
CG
|
D:PRO168
|
4.1
|
20.1
|
1.0
|
|
HE22
|
D:GLN192
|
4.1
|
17.0
|
1.0
|
|
CB
|
D:GLN192
|
4.2
|
19.8
|
1.0
|
|
N
|
D:GLN192
|
4.2
|
22.1
|
1.0
|
|
O
|
D:THR190
|
4.2
|
36.2
|
1.0
|
|
CA
|
D:LEU167
|
4.2
|
17.2
|
1.0
|
|
O
|
D:HOH539
|
4.3
|
32.7
|
1.0
|
|
HD2
|
D:PRO168
|
4.3
|
19.8
|
1.0
|
|
HG2
|
D:PRO168
|
4.3
|
20.1
|
1.0
|
|
HE2
|
D:MET165
|
4.3
|
22.6
|
1.0
|
|
HD21
|
D:LEU167
|
4.4
|
16.8
|
1.0
|
|
HD22
|
D:LEU167
|
4.4
|
16.8
|
1.0
|
|
C
|
D:GLN192
|
4.4
|
22.0
|
1.0
|
|
CG
|
D:GLN192
|
4.4
|
18.3
|
1.0
|
|
CA
|
D:GLN192
|
4.5
|
21.4
|
1.0
|
|
N
|
D:PRO168
|
4.5
|
20.2
|
1.0
|
|
CE
|
D:MET165
|
4.5
|
22.3
|
1.0
|
|
NE2
|
D:GLN192
|
4.6
|
16.9
|
1.0
|
|
C14
|
D:4WI401
|
4.6
|
20.7
|
1.0
|
|
C
|
D:GLU166
|
4.7
|
18.7
|
1.0
|
|
HE1
|
D:MET165
|
4.7
|
22.5
|
1.0
|
|
H20
|
D:4WI401
|
4.7
|
20.7
|
1.0
|
|
C
|
D:LEU167
|
4.8
|
18.2
|
1.0
|
|
CD
|
D:GLN192
|
4.8
|
17.3
|
1.0
|
|
HG
|
D:LEU167
|
4.8
|
16.9
|
1.0
|
|
H15
|
D:4WI401
|
4.9
|
20.9
|
1.0
|
|
CG
|
D:LEU167
|
4.9
|
16.9
|
1.0
|
|
N
|
D:LEU167
|
4.9
|
18.0
|
1.0
|
|
HA
|
D:ALA191
|
4.9
|
28.5
|
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 17:41:41 2024
|
