Fluorine in PDB 8hur: Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622:
3.4.22.69;
Protein crystallography data
The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622, PDB code: 8hur
was solved by
X.L.Zhou,
J.Zhang,
J.Li,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.58 /
1.64
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.72,
98.965,
59.359,
90,
108.48,
90
|
R / Rfree (%)
|
20.1 /
22.6
|
Other elements in 8hur:
The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
(pdb code 8hur). 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 S217622, PDB code: 8hur:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8hur
Go back to
Fluorine Binding Sites List in 8hur
Fluorine binding site 1 out
of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
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 S217622 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:31.5
occ:1.00
|
F28
|
A:7YY401
|
0.0
|
31.5
|
1.0
|
C27
|
A:7YY401
|
1.4
|
30.1
|
1.0
|
C26
|
A:7YY401
|
2.3
|
23.9
|
1.0
|
C29
|
A:7YY401
|
2.4
|
28.4
|
1.0
|
C25
|
A:7YY401
|
2.8
|
25.4
|
1.0
|
CG
|
A:GLN189
|
3.3
|
34.9
|
1.0
|
CA
|
A:GLN189
|
3.3
|
32.5
|
1.0
|
CB
|
A:GLN189
|
3.4
|
29.1
|
1.0
|
C30
|
A:7YY401
|
3.6
|
26.8
|
1.0
|
C34
|
A:7YY401
|
3.6
|
25.3
|
1.0
|
CD
|
A:GLN189
|
3.9
|
40.7
|
1.0
|
NE2
|
A:GLN189
|
4.0
|
46.0
|
1.0
|
N
|
A:GLN189
|
4.0
|
32.8
|
1.0
|
C32
|
A:7YY401
|
4.1
|
26.7
|
1.0
|
O
|
A:ARG188
|
4.1
|
28.5
|
1.0
|
N24
|
A:7YY401
|
4.2
|
25.7
|
1.0
|
C
|
A:ARG188
|
4.3
|
32.8
|
1.0
|
CB
|
A:MET165
|
4.4
|
25.6
|
1.0
|
O36
|
A:7YY401
|
4.5
|
24.6
|
1.0
|
C
|
A:GLN189
|
4.5
|
36.2
|
1.0
|
NE2
|
A:HIS41
|
4.7
|
25.4
|
1.0
|
F31
|
A:7YY401
|
4.7
|
29.5
|
1.0
|
SD
|
A:MET165
|
4.8
|
32.6
|
1.0
|
OE1
|
A:GLN189
|
4.8
|
41.7
|
1.0
|
C35
|
A:7YY401
|
4.9
|
25.6
|
1.0
|
N
|
A:THR190
|
4.9
|
35.4
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8hur
Go back to
Fluorine Binding Sites List in 8hur
Fluorine binding site 2 out
of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
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 S217622 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:29.5
occ:1.00
|
F31
|
A:7YY401
|
0.0
|
29.5
|
1.0
|
C30
|
A:7YY401
|
1.4
|
26.8
|
1.0
|
C29
|
A:7YY401
|
2.4
|
28.4
|
1.0
|
C32
|
A:7YY401
|
2.4
|
26.7
|
1.0
|
F33
|
A:7YY401
|
2.7
|
25.9
|
1.0
|
CA
|
A:ASP187
|
3.0
|
28.9
|
1.0
|
CB
|
A:ASP187
|
3.1
|
26.3
|
1.0
|
C
|
A:ASP187
|
3.2
|
30.1
|
1.0
|
ND1
|
A:HIS41
|
3.6
|
27.6
|
1.0
|
O
|
A:ASP187
|
3.6
|
29.1
|
1.0
|
C27
|
A:7YY401
|
3.6
|
30.1
|
1.0
|
C34
|
A:7YY401
|
3.6
|
25.3
|
1.0
|
N
|
A:ARG188
|
3.7
|
27.2
|
1.0
|
CG
|
A:HIS41
|
3.8
|
22.7
|
1.0
|
CE1
|
A:HIS41
|
4.0
|
26.6
|
1.0
|
SD
|
A:MET165
|
4.0
|
32.6
|
1.0
|
C26
|
A:7YY401
|
4.1
|
23.9
|
1.0
|
CB
|
A:HIS41
|
4.2
|
23.5
|
1.0
|
CD2
|
A:HIS41
|
4.3
|
26.6
|
1.0
|
NE2
|
A:HIS41
|
4.3
|
25.4
|
1.0
|
O
|
A:HOH542
|
4.4
|
23.2
|
1.0
|
N
|
A:ASP187
|
4.4
|
24.8
|
1.0
|
CG
|
A:ASP187
|
4.5
|
26.8
|
1.0
|
CA
|
A:ARG188
|
4.5
|
31.0
|
1.0
|
CD2
|
A:HIS164
|
4.5
|
22.6
|
1.0
|
O
|
A:ARG188
|
4.6
|
28.5
|
1.0
|
OH
|
A:TYR54
|
4.6
|
28.4
|
1.0
|
C
|
A:ARG188
|
4.6
|
32.8
|
1.0
|
O
|
A:VAL186
|
4.6
|
24.9
|
1.0
|
CB
|
A:HIS164
|
4.6
|
24.2
|
1.0
|
F28
|
A:7YY401
|
4.7
|
31.5
|
1.0
|
CB
|
A:MET165
|
4.8
|
25.6
|
1.0
|
CG
|
A:MET165
|
5.0
|
24.3
|
1.0
|
C
|
A:VAL186
|
5.0
|
26.4
|
1.0
|
CG
|
A:HIS164
|
5.0
|
24.2
|
1.0
|
OD2
|
A:ASP187
|
5.0
|
26.6
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8hur
Go back to
Fluorine Binding Sites List in 8hur
Fluorine binding site 3 out
of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
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 S217622 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:25.9
occ:1.00
|
F33
|
A:7YY401
|
0.0
|
25.9
|
1.0
|
C32
|
A:7YY401
|
1.4
|
26.7
|
1.0
|
C30
|
A:7YY401
|
2.4
|
26.8
|
1.0
|
C34
|
A:7YY401
|
2.4
|
25.3
|
1.0
|
F31
|
A:7YY401
|
2.7
|
29.5
|
1.0
|
O
|
A:HIS164
|
3.3
|
24.1
|
1.0
|
SG
|
A:CYS145
|
3.4
|
23.3
|
1.0
|
CB
|
A:HIS41
|
3.4
|
23.5
|
1.0
|
CG
|
A:HIS41
|
3.5
|
22.7
|
1.0
|
CD2
|
A:HIS41
|
3.6
|
26.6
|
1.0
|
C29
|
A:7YY401
|
3.6
|
28.4
|
1.0
|
C26
|
A:7YY401
|
3.6
|
23.9
|
1.0
|
C
|
A:HIS164
|
3.8
|
22.4
|
1.0
|
CB
|
A:HIS164
|
3.8
|
24.2
|
1.0
|
CA
|
A:HIS164
|
3.9
|
23.6
|
1.0
|
CD2
|
A:HIS164
|
4.0
|
22.6
|
1.0
|
C27
|
A:7YY401
|
4.1
|
30.1
|
1.0
|
CG
|
A:HIS164
|
4.2
|
24.2
|
1.0
|
O
|
A:HOH542
|
4.2
|
23.2
|
1.0
|
ND1
|
A:HIS41
|
4.3
|
27.6
|
1.0
|
CL2
|
A:7YY401
|
4.3
|
27.3
|
1.0
|
NE2
|
A:HIS41
|
4.4
|
25.4
|
1.0
|
CB
|
A:PRO39
|
4.7
|
20.1
|
1.0
|
CE1
|
A:HIS41
|
4.7
|
26.6
|
1.0
|
N
|
A:MET165
|
4.8
|
23.7
|
1.0
|
CB
|
A:CYS145
|
4.9
|
19.4
|
1.0
|
CB
|
A:MET165
|
4.9
|
25.6
|
1.0
|
CA
|
A:HIS41
|
4.9
|
24.3
|
1.0
|
C25
|
A:7YY401
|
4.9
|
25.4
|
1.0
|
CB
|
A:ASP187
|
5.0
|
26.3
|
1.0
|
N24
|
A:7YY401
|
5.0
|
25.7
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8hur
Go back to
Fluorine Binding Sites List in 8hur
Fluorine binding site 4 out
of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
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 S217622 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:29.4
occ:1.00
|
F28
|
B:7YY401
|
0.0
|
29.4
|
1.0
|
C27
|
B:7YY401
|
1.4
|
26.9
|
1.0
|
C26
|
B:7YY401
|
2.4
|
24.9
|
1.0
|
C29
|
B:7YY401
|
2.4
|
25.1
|
1.0
|
C25
|
B:7YY401
|
2.9
|
26.6
|
1.0
|
CA
|
B:GLN189
|
3.3
|
29.5
|
1.0
|
CG
|
B:GLN189
|
3.4
|
30.4
|
1.0
|
CE
|
B:MET165
|
3.5
|
37.8
|
1.0
|
CB
|
B:GLN189
|
3.5
|
31.6
|
1.0
|
C30
|
B:7YY401
|
3.6
|
26.4
|
1.0
|
O
|
B:HOH532
|
3.6
|
26.4
|
1.0
|
C34
|
B:7YY401
|
3.7
|
26.3
|
1.0
|
N
|
B:GLN189
|
3.9
|
28.5
|
1.0
|
O
|
B:ARG188
|
4.0
|
27.2
|
1.0
|
C32
|
B:7YY401
|
4.1
|
25.1
|
1.0
|
C
|
B:ARG188
|
4.2
|
28.9
|
1.0
|
N24
|
B:7YY401
|
4.3
|
23.3
|
1.0
|
CB
|
B:MET165
|
4.4
|
24.1
|
1.0
|
SD
|
B:MET165
|
4.5
|
41.2
|
1.0
|
CD
|
B:GLN189
|
4.5
|
35.0
|
1.0
|
C
|
B:GLN189
|
4.6
|
34.0
|
1.0
|
O36
|
B:7YY401
|
4.7
|
24.4
|
1.0
|
NE2
|
B:HIS41
|
4.7
|
28.1
|
1.0
|
F31
|
B:7YY401
|
4.7
|
29.0
|
1.0
|
OE1
|
B:GLN189
|
4.8
|
39.7
|
1.0
|
N
|
B:THR190
|
4.9
|
29.0
|
1.0
|
C35
|
B:7YY401
|
5.0
|
24.4
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8hur
Go back to
Fluorine Binding Sites List in 8hur
Fluorine binding site 5 out
of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
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 S217622 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:29.0
occ:1.00
|
F31
|
B:7YY401
|
0.0
|
29.0
|
1.0
|
C30
|
B:7YY401
|
1.4
|
26.4
|
1.0
|
C29
|
B:7YY401
|
2.3
|
25.1
|
1.0
|
C32
|
B:7YY401
|
2.4
|
25.1
|
1.0
|
CE
|
B:MET165
|
2.7
|
37.8
|
1.0
|
F33
|
B:7YY401
|
2.8
|
23.2
|
1.0
|
CA
|
B:ASP187
|
2.9
|
20.3
|
1.0
|
CB
|
B:ASP187
|
3.0
|
22.0
|
1.0
|
C
|
B:ASP187
|
3.1
|
24.9
|
1.0
|
N
|
B:ARG188
|
3.5
|
24.7
|
1.0
|
C27
|
B:7YY401
|
3.6
|
26.9
|
1.0
|
O
|
B:ASP187
|
3.6
|
27.6
|
1.0
|
ND1
|
B:HIS41
|
3.6
|
24.5
|
1.0
|
C34
|
B:7YY401
|
3.6
|
26.3
|
1.0
|
CG
|
B:HIS41
|
3.8
|
26.3
|
1.0
|
CE1
|
B:HIS41
|
3.9
|
27.3
|
1.0
|
C26
|
B:7YY401
|
4.1
|
24.9
|
1.0
|
CD2
|
B:HIS41
|
4.2
|
26.8
|
1.0
|
NE2
|
B:HIS41
|
4.2
|
28.1
|
1.0
|
CB
|
B:HIS41
|
4.3
|
25.2
|
1.0
|
N
|
B:ASP187
|
4.3
|
23.5
|
1.0
|
SD
|
B:MET165
|
4.4
|
41.2
|
1.0
|
O
|
B:HOH553
|
4.4
|
24.1
|
1.0
|
CA
|
B:ARG188
|
4.4
|
28.0
|
1.0
|
CG
|
B:ASP187
|
4.4
|
22.0
|
1.0
|
OH
|
B:TYR54
|
4.5
|
28.7
|
1.0
|
CD2
|
B:HIS164
|
4.5
|
19.9
|
1.0
|
O
|
B:VAL186
|
4.6
|
24.1
|
1.0
|
C
|
B:ARG188
|
4.6
|
28.9
|
1.0
|
O
|
B:ARG188
|
4.7
|
27.2
|
1.0
|
F28
|
B:7YY401
|
4.7
|
29.4
|
1.0
|
CB
|
B:HIS164
|
4.7
|
24.4
|
1.0
|
CB
|
B:MET165
|
4.8
|
24.1
|
1.0
|
C
|
B:VAL186
|
4.9
|
22.8
|
1.0
|
CG
|
B:MET165
|
4.9
|
27.6
|
1.0
|
OD2
|
B:ASP187
|
5.0
|
22.6
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 8hur
Go back to
Fluorine Binding Sites List in 8hur
Fluorine binding site 6 out
of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622
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 S217622 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:23.2
occ:1.00
|
F33
|
B:7YY401
|
0.0
|
23.2
|
1.0
|
C32
|
B:7YY401
|
1.4
|
25.1
|
1.0
|
C34
|
B:7YY401
|
2.4
|
26.3
|
1.0
|
C30
|
B:7YY401
|
2.4
|
26.4
|
1.0
|
F31
|
B:7YY401
|
2.8
|
29.0
|
1.0
|
O
|
B:HIS164
|
3.3
|
23.4
|
1.0
|
SG
|
B:CYS145
|
3.4
|
23.2
|
1.0
|
CB
|
B:HIS41
|
3.4
|
25.2
|
1.0
|
CG
|
B:HIS41
|
3.5
|
26.3
|
1.0
|
CD2
|
B:HIS41
|
3.5
|
26.8
|
1.0
|
C26
|
B:7YY401
|
3.7
|
24.9
|
1.0
|
C29
|
B:7YY401
|
3.7
|
25.1
|
1.0
|
C
|
B:HIS164
|
3.8
|
23.9
|
1.0
|
CD2
|
B:HIS164
|
3.9
|
19.9
|
1.0
|
CB
|
B:HIS164
|
3.9
|
24.4
|
1.0
|
CA
|
B:HIS164
|
4.0
|
21.3
|
1.0
|
CG
|
B:HIS164
|
4.1
|
20.1
|
1.0
|
C27
|
B:7YY401
|
4.2
|
26.9
|
1.0
|
O
|
B:HOH553
|
4.2
|
24.1
|
1.0
|
ND1
|
B:HIS41
|
4.2
|
24.5
|
1.0
|
CL2
|
B:7YY401
|
4.3
|
25.0
|
1.0
|
NE2
|
B:HIS41
|
4.4
|
28.1
|
1.0
|
CE
|
B:MET165
|
4.4
|
37.8
|
1.0
|
CE1
|
B:HIS41
|
4.7
|
27.3
|
1.0
|
CB
|
B:PRO39
|
4.8
|
19.6
|
1.0
|
N
|
B:MET165
|
4.8
|
21.2
|
1.0
|
CB
|
B:MET165
|
4.9
|
24.1
|
1.0
|
CA
|
B:HIS41
|
4.9
|
22.3
|
1.0
|
C25
|
B:7YY401
|
4.9
|
26.6
|
1.0
|
CB
|
B:CYS145
|
4.9
|
21.3
|
1.0
|
CB
|
B:ASP187
|
5.0
|
22.0
|
1.0
|
N24
|
B:7YY401
|
5.0
|
23.3
|
1.0
|
|
Reference:
X.L.Zhou,
J.Zhang,
J.Li.
Crystal Structure of Sars-Cov-2 Main Protease in Complex with S217622 To Be Published.
Page generated: Fri Aug 2 20:17:00 2024
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