Fluorine in PDB 5srp: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer
Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer
All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer:
3.4.19.121;
Protein crystallography data
The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer, PDB code: 5srp
was solved by
G.J.Correy,
J.S.Fraser,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.69 /
1.05
|
Space group
|
P 43
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.757,
88.757,
39.644,
90,
90,
90
|
R / Rfree (%)
|
13.2 /
15
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer
(pdb code 5srp). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer, PDB code: 5srp:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 5srp
Go back to
Fluorine Binding Sites List in 5srp
Fluorine binding site 1 out
of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F202
b:9.3
occ:0.14
|
F1
|
A:TFA202
|
0.0
|
9.3
|
0.1
|
C2
|
A:TFA202
|
1.4
|
8.3
|
0.1
|
F2
|
A:TFA202
|
2.2
|
8.8
|
0.1
|
F3
|
A:TFA202
|
2.2
|
8.9
|
0.1
|
O
|
A:HOH543
|
2.3
|
39.8
|
0.7
|
O
|
A:HOH419
|
2.3
|
23.6
|
0.7
|
C1
|
A:TFA202
|
2.4
|
6.4
|
0.1
|
O2
|
A:RDN201
|
2.4
|
13.6
|
0.1
|
O
|
A:TFA202
|
2.7
|
7.1
|
0.1
|
HD22
|
A:LEU160
|
2.7
|
23.3
|
0.7
|
HD23
|
A:LEU160
|
2.8
|
21.6
|
0.3
|
H1
|
A:RDN201
|
2.8
|
15.6
|
0.1
|
HD23
|
A:LEU160
|
2.8
|
23.3
|
0.7
|
O
|
A:HOH310
|
3.0
|
16.6
|
0.3
|
H
|
A:GLY130
|
3.0
|
12.7
|
0.7
|
CD2
|
A:LEU160
|
3.0
|
19.4
|
0.7
|
H
|
A:GLY130
|
3.0
|
14.2
|
0.3
|
HD21
|
A:LEU160
|
3.1
|
23.3
|
0.7
|
C1
|
A:RDN201
|
3.1
|
13.3
|
0.1
|
HB1
|
A:ALA129
|
3.2
|
13.6
|
0.7
|
HA2
|
A:GLY130
|
3.2
|
14.3
|
0.3
|
O
|
A:HOH458
|
3.2
|
22.5
|
0.7
|
C2
|
A:RDN201
|
3.4
|
13.0
|
0.1
|
CD2
|
A:LEU160
|
3.5
|
18.0
|
0.3
|
HA2
|
A:GLY130
|
3.5
|
13.3
|
0.7
|
HD22
|
A:LEU160
|
3.5
|
21.6
|
0.3
|
N
|
A:GLY130
|
3.5
|
11.8
|
0.3
|
OXT
|
A:TFA202
|
3.5
|
5.0
|
0.1
|
HD21
|
A:LEU160
|
3.6
|
21.6
|
0.3
|
N
|
A:GLY130
|
3.6
|
10.6
|
0.7
|
HA3
|
A:GLY130
|
3.6
|
14.3
|
0.3
|
CA
|
A:GLY130
|
3.6
|
11.9
|
0.3
|
HB1
|
A:ALA129
|
3.7
|
11.5
|
0.3
|
CA
|
A:GLY130
|
4.0
|
11.1
|
0.7
|
CB
|
A:ALA129
|
4.0
|
11.3
|
0.7
|
O1
|
A:RDN201
|
4.1
|
13.0
|
0.1
|
HB3
|
A:PRO136
|
4.1
|
18.8
|
0.7
|
HB3
|
A:ALA129
|
4.1
|
13.6
|
0.7
|
HB3
|
A:PRO136
|
4.1
|
19.1
|
0.3
|
HA3
|
A:GLY130
|
4.1
|
13.3
|
0.7
|
HG3
|
A:PRO136
|
4.1
|
20.3
|
0.7
|
O
|
A:HOH536
|
4.1
|
30.3
|
0.7
|
H3
|
A:RDN201
|
4.2
|
15.3
|
0.1
|
HB3
|
A:ALA129
|
4.2
|
11.5
|
0.3
|
H13
|
A:RDN201
|
4.3
|
15.9
|
0.1
|
HB2
|
A:ASP157
|
4.4
|
17.9
|
0.3
|
CB
|
A:ALA129
|
4.4
|
9.6
|
0.3
|
C3
|
A:RDN201
|
4.4
|
12.8
|
0.1
|
HB3
|
A:ASP157
|
4.5
|
17.9
|
0.3
|
O
|
A:HOH515
|
4.5
|
31.9
|
0.7
|
CG
|
A:LEU160
|
4.5
|
19.6
|
0.7
|
O
|
A:HOH542
|
4.5
|
27.6
|
0.9
|
H
|
A:ASP157
|
4.5
|
16.6
|
0.3
|
C
|
A:ALA129
|
4.6
|
11.6
|
0.3
|
C
|
A:ALA129
|
4.6
|
9.8
|
0.7
|
O
|
A:HOH472
|
4.6
|
38.8
|
0.7
|
HB2
|
A:ALA129
|
4.7
|
13.6
|
0.7
|
HG13
|
A:VAL155
|
4.7
|
18.9
|
0.7
|
HB3
|
A:LEU160
|
4.7
|
21.2
|
0.3
|
C15
|
A:RDN201
|
4.7
|
12.6
|
0.1
|
HG3
|
A:PRO136
|
4.7
|
19.3
|
0.3
|
CB
|
A:PRO136
|
4.8
|
15.6
|
0.7
|
CG
|
A:LEU160
|
4.8
|
17.8
|
0.3
|
HB2
|
A:LEU160
|
4.9
|
22.6
|
0.7
|
CA
|
A:ALA129
|
4.9
|
9.8
|
0.7
|
CG
|
A:PRO136
|
4.9
|
16.9
|
0.7
|
HB3
|
A:LEU160
|
4.9
|
22.6
|
0.7
|
CB
|
A:ASP157
|
4.9
|
14.9
|
0.3
|
HB3
|
A:ASP157
|
4.9
|
25.9
|
0.7
|
HB3
|
A:PHE156
|
5.0
|
14.1
|
0.3
|
C16
|
A:RDN201
|
5.0
|
13.3
|
0.1
|
HB2
|
A:LEU160
|
5.0
|
21.2
|
0.3
|
HG
|
A:LEU160
|
5.0
|
23.5
|
0.7
|
|
Fluorine binding site 2 out
of 3 in 5srp
Go back to
Fluorine Binding Sites List in 5srp
Fluorine binding site 2 out
of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F202
b:8.8
occ:0.14
|
F2
|
A:TFA202
|
0.0
|
8.8
|
0.1
|
H1
|
A:RDN201
|
1.2
|
15.6
|
0.1
|
C2
|
A:TFA202
|
1.4
|
8.3
|
0.1
|
O
|
A:HOH543
|
2.0
|
39.8
|
0.7
|
C2
|
A:RDN201
|
2.0
|
13.0
|
0.1
|
O
|
A:HOH536
|
2.1
|
30.3
|
0.7
|
F1
|
A:TFA202
|
2.2
|
9.3
|
0.1
|
F3
|
A:TFA202
|
2.2
|
8.9
|
0.1
|
H13
|
A:RDN201
|
2.3
|
15.9
|
0.1
|
C1
|
A:TFA202
|
2.4
|
6.4
|
0.1
|
C1
|
A:RDN201
|
2.5
|
13.3
|
0.1
|
O2
|
A:RDN201
|
2.8
|
13.6
|
0.1
|
C15
|
A:RDN201
|
2.8
|
12.6
|
0.1
|
OXT
|
A:TFA202
|
2.8
|
5.0
|
0.1
|
C16
|
A:RDN201
|
2.9
|
13.3
|
0.1
|
HB3
|
A:ALA129
|
2.9
|
13.6
|
0.7
|
HB1
|
A:ALA129
|
2.9
|
13.6
|
0.7
|
HA3
|
A:GLY130
|
3.0
|
14.3
|
0.3
|
H
|
A:GLY130
|
3.1
|
12.7
|
0.7
|
O
|
A:HOH542
|
3.2
|
27.6
|
0.9
|
N
|
A:GLY130
|
3.2
|
10.6
|
0.7
|
HA3
|
A:GLY130
|
3.3
|
13.3
|
0.7
|
C3
|
A:RDN201
|
3.3
|
12.8
|
0.1
|
O
|
A:TFA202
|
3.3
|
7.1
|
0.1
|
O1
|
A:RDN201
|
3.3
|
13.0
|
0.1
|
CB
|
A:ALA129
|
3.4
|
11.3
|
0.7
|
O
|
A:HOH472
|
3.4
|
38.8
|
0.7
|
HB3
|
A:ALA129
|
3.4
|
11.5
|
0.3
|
H
|
A:GLY130
|
3.5
|
14.2
|
0.3
|
N
|
A:GLY130
|
3.5
|
11.8
|
0.3
|
O
|
A:HOH344
|
3.5
|
16.4
|
0.9
|
C14
|
A:RDN201
|
3.5
|
12.3
|
0.1
|
H3
|
A:RDN201
|
3.6
|
15.3
|
0.1
|
H12
|
A:RDN201
|
3.6
|
15.9
|
0.1
|
CA
|
A:GLY130
|
3.6
|
11.9
|
0.3
|
H10
|
A:RDN201
|
3.6
|
14.7
|
0.1
|
CA
|
A:GLY130
|
3.6
|
11.1
|
0.7
|
O
|
A:HOH458
|
3.6
|
22.5
|
0.7
|
HA2
|
A:GLY130
|
3.6
|
13.3
|
0.7
|
HA2
|
A:GLY130
|
3.7
|
14.3
|
0.3
|
H15
|
A:RDN201
|
3.7
|
16.4
|
0.1
|
O
|
A:HOH419
|
3.8
|
23.6
|
0.7
|
N1
|
A:RDN201
|
3.8
|
11.6
|
0.1
|
C
|
A:ALA129
|
3.8
|
9.8
|
0.7
|
HB1
|
A:ALA129
|
3.8
|
11.5
|
0.3
|
C17
|
A:RDN201
|
3.9
|
13.6
|
0.1
|
H2
|
A:RDN201
|
4.0
|
15.3
|
0.1
|
CB
|
A:ALA129
|
4.1
|
9.6
|
0.3
|
C
|
A:ALA129
|
4.1
|
11.6
|
0.3
|
C18
|
A:RDN201
|
4.1
|
13.3
|
0.1
|
HB2
|
A:ALA129
|
4.1
|
13.6
|
0.7
|
CA
|
A:ALA129
|
4.2
|
9.8
|
0.7
|
HB2
|
A:LEU126
|
4.2
|
16.3
|
0.3
|
O
|
A:HOH412
|
4.3
|
27.8
|
0.3
|
O
|
A:HOH383
|
4.3
|
14.2
|
0.9
|
O
|
A:HOH310
|
4.3
|
16.6
|
0.3
|
HD23
|
A:LEU160
|
4.3
|
23.3
|
0.7
|
H11
|
A:RDN201
|
4.4
|
14.7
|
0.1
|
H16
|
A:RDN201
|
4.4
|
15.9
|
0.1
|
HB2
|
A:LEU126
|
4.5
|
13.1
|
0.7
|
O
|
A:HOH544
|
4.5
|
57.3
|
0.9
|
O
|
A:ALA129
|
4.5
|
9.4
|
0.7
|
O
|
A:LEU126
|
4.5
|
11.1
|
0.3
|
HD21
|
A:LEU160
|
4.6
|
23.3
|
0.7
|
O
|
A:ALA129
|
4.6
|
12.3
|
0.3
|
HD23
|
A:LEU160
|
4.6
|
21.6
|
0.3
|
O
|
A:HOH500
|
4.7
|
16.9
|
0.3
|
HB3
|
A:PHE156
|
4.7
|
14.1
|
0.3
|
HD22
|
A:LEU160
|
4.7
|
23.3
|
0.7
|
CA
|
A:ALA129
|
4.7
|
10.0
|
0.3
|
H
|
A:PHE156
|
4.7
|
14.9
|
0.3
|
H14
|
A:RDN201
|
4.7
|
16.4
|
0.1
|
CD2
|
A:LEU160
|
4.7
|
19.4
|
0.7
|
H
|
A:LEU126
|
4.8
|
15.1
|
0.3
|
HA
|
A:ALA129
|
4.8
|
11.8
|
0.7
|
O
|
A:HOH443
|
4.8
|
13.9
|
0.7
|
HB2
|
A:ALA129
|
4.9
|
11.5
|
0.3
|
H17
|
A:RDN201
|
4.9
|
15.9
|
0.1
|
HB3
|
A:PRO136
|
4.9
|
18.8
|
0.7
|
O
|
A:LEU126
|
5.0
|
11.1
|
0.7
|
|
Fluorine binding site 3 out
of 3 in 5srp
Go back to
Fluorine Binding Sites List in 5srp
Fluorine binding site 3 out
of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5340019182 - (R) Isomer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F202
b:8.9
occ:0.14
|
F3
|
A:TFA202
|
0.0
|
8.9
|
0.1
|
O
|
A:HOH543
|
1.3
|
39.8
|
0.7
|
C2
|
A:TFA202
|
1.4
|
8.3
|
0.1
|
F1
|
A:TFA202
|
2.2
|
9.3
|
0.1
|
F2
|
A:TFA202
|
2.2
|
8.8
|
0.1
|
C1
|
A:TFA202
|
2.3
|
6.4
|
0.1
|
HB1
|
A:ALA129
|
2.5
|
13.6
|
0.7
|
HD21
|
A:LEU160
|
2.7
|
23.3
|
0.7
|
OXT
|
A:TFA202
|
2.9
|
5.0
|
0.1
|
HD23
|
A:LEU160
|
2.9
|
23.3
|
0.7
|
HB3
|
A:ALA129
|
2.9
|
13.6
|
0.7
|
O2
|
A:RDN201
|
3.0
|
13.6
|
0.1
|
HB2
|
A:LEU126
|
3.0
|
16.3
|
0.3
|
C1
|
A:RDN201
|
3.0
|
13.3
|
0.1
|
CB
|
A:ALA129
|
3.1
|
11.3
|
0.7
|
H13
|
A:RDN201
|
3.1
|
15.9
|
0.1
|
HB3
|
A:ALA129
|
3.1
|
11.5
|
0.3
|
HD21
|
A:LEU160
|
3.1
|
21.6
|
0.3
|
HB3
|
A:PRO136
|
3.2
|
18.8
|
0.7
|
CD2
|
A:LEU160
|
3.2
|
19.4
|
0.7
|
HD23
|
A:LEU160
|
3.2
|
21.6
|
0.3
|
HB1
|
A:ALA129
|
3.2
|
11.5
|
0.3
|
H1
|
A:RDN201
|
3.2
|
15.6
|
0.1
|
HD12
|
A:LEU126
|
3.2
|
17.0
|
0.7
|
O
|
A:TFA202
|
3.3
|
7.1
|
0.1
|
HB2
|
A:LEU126
|
3.3
|
13.1
|
0.7
|
O1
|
A:RDN201
|
3.4
|
13.0
|
0.1
|
HB3
|
A:PRO136
|
3.4
|
19.1
|
0.3
|
HD12
|
A:LEU126
|
3.4
|
18.3
|
0.3
|
HB2
|
A:ALA129
|
3.4
|
13.6
|
0.7
|
HD22
|
A:LEU160
|
3.5
|
23.3
|
0.7
|
O
|
A:HOH419
|
3.6
|
23.6
|
0.7
|
CB
|
A:ALA129
|
3.6
|
9.6
|
0.3
|
CD2
|
A:LEU160
|
3.6
|
18.0
|
0.3
|
C2
|
A:RDN201
|
3.6
|
13.0
|
0.1
|
O
|
A:HOH383
|
3.7
|
14.2
|
0.9
|
O
|
A:HOH536
|
3.7
|
30.3
|
0.7
|
H15
|
A:RDN201
|
3.7
|
16.4
|
0.1
|
O
|
A:HOH458
|
3.8
|
22.5
|
0.7
|
H
|
A:GLY130
|
3.8
|
12.7
|
0.7
|
HG13
|
A:VAL155
|
3.8
|
18.9
|
0.7
|
H
|
A:GLY130
|
3.8
|
14.2
|
0.3
|
CB
|
A:LEU126
|
3.9
|
13.6
|
0.3
|
C16
|
A:RDN201
|
3.9
|
13.3
|
0.1
|
HB3
|
A:LEU126
|
3.9
|
16.3
|
0.3
|
CB
|
A:PRO136
|
4.0
|
15.6
|
0.7
|
HG13
|
A:VAL155
|
4.0
|
15.7
|
0.3
|
HD22
|
A:LEU160
|
4.1
|
21.6
|
0.3
|
HB2
|
A:PRO136
|
4.1
|
18.8
|
0.7
|
O
|
A:HOH310
|
4.1
|
16.6
|
0.3
|
CD1
|
A:LEU126
|
4.1
|
14.2
|
0.7
|
HD13
|
A:LEU126
|
4.1
|
18.3
|
0.3
|
HB2
|
A:ALA129
|
4.1
|
11.5
|
0.3
|
CD1
|
A:LEU126
|
4.1
|
15.3
|
0.3
|
O
|
A:HOH472
|
4.2
|
38.8
|
0.7
|
HD13
|
A:LEU126
|
4.2
|
17.0
|
0.7
|
CB
|
A:LEU126
|
4.2
|
10.9
|
0.7
|
N
|
A:GLY130
|
4.3
|
11.8
|
0.3
|
CB
|
A:PRO136
|
4.3
|
15.9
|
0.3
|
C15
|
A:RDN201
|
4.3
|
12.6
|
0.1
|
C17
|
A:RDN201
|
4.3
|
13.6
|
0.1
|
HG3
|
A:PRO136
|
4.3
|
20.3
|
0.7
|
N
|
A:GLY130
|
4.3
|
10.6
|
0.7
|
H
|
A:LEU126
|
4.4
|
15.1
|
0.3
|
HB2
|
A:PRO136
|
4.4
|
19.1
|
0.3
|
HB3
|
A:LEU126
|
4.4
|
13.1
|
0.7
|
CA
|
A:ALA129
|
4.5
|
9.8
|
0.7
|
HD11
|
A:LEU164
|
4.5
|
19.9
|
1.0
|
HG22
|
A:VAL155
|
4.5
|
18.6
|
0.7
|
CG
|
A:LEU160
|
4.5
|
19.6
|
0.7
|
CG
|
A:LEU126
|
4.6
|
14.6
|
0.3
|
O
|
A:LEU126
|
4.6
|
11.1
|
0.3
|
H
|
A:LEU126
|
4.6
|
12.3
|
0.7
|
HG
|
A:LEU160
|
4.6
|
23.5
|
0.7
|
O
|
A:HOH344
|
4.7
|
16.4
|
0.9
|
H
|
A:PHE156
|
4.7
|
14.9
|
0.3
|
CG
|
A:LEU126
|
4.7
|
12.6
|
0.7
|
CG1
|
A:VAL155
|
4.7
|
15.7
|
0.7
|
H12
|
A:RDN201
|
4.7
|
15.9
|
0.1
|
CG
|
A:PRO136
|
4.8
|
16.9
|
0.7
|
HG
|
A:LEU160
|
4.8
|
21.4
|
0.3
|
HA3
|
A:GLY130
|
4.8
|
14.3
|
0.3
|
HA
|
A:PRO136
|
4.8
|
18.7
|
0.3
|
C
|
A:ALA129
|
4.8
|
9.8
|
0.7
|
HG11
|
A:VAL155
|
4.8
|
18.9
|
0.7
|
HD11
|
A:LEU126
|
4.8
|
17.0
|
0.7
|
HA
|
A:ALA129
|
4.8
|
11.8
|
0.7
|
C
|
A:ALA129
|
4.8
|
11.6
|
0.3
|
CA
|
A:ALA129
|
4.8
|
10.0
|
0.3
|
CG
|
A:LEU160
|
4.8
|
17.8
|
0.3
|
HG
|
A:LEU126
|
4.9
|
17.5
|
0.3
|
HA2
|
A:GLY130
|
4.9
|
14.3
|
0.3
|
HA
|
A:VAL155
|
4.9
|
17.9
|
0.7
|
HA
|
A:VAL155
|
4.9
|
15.3
|
0.3
|
HG
|
A:LEU126
|
4.9
|
15.1
|
0.7
|
HD11
|
A:LEU126
|
4.9
|
18.3
|
0.3
|
CA
|
A:GLY130
|
4.9
|
11.9
|
0.3
|
CA
|
A:LEU126
|
4.9
|
12.1
|
0.3
|
HA
|
A:PRO136
|
4.9
|
17.6
|
0.7
|
HG3
|
A:PRO136
|
5.0
|
19.3
|
0.3
|
HD11
|
A:LEU160
|
5.0
|
24.6
|
0.7
|
|
Reference:
G.J.Correy,
J.S.Fraser.
Ligand Screen Against Sars-Cov-2 NSP3 Macrodomain To Be Published.
Page generated: Thu Aug 1 14:52:55 2024
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