Fluorine in PDB 5sq1: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC001601221314 - (S) Isomer
Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC001601221314 - (S) Isomer
All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC001601221314 - (S) 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 ZINC001601221314 - (S) Isomer, PDB code: 5sq1
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)
|
36.13 /
1.05
|
|
Space group
|
P 43
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.824,
88.824,
39.55,
90,
90,
90
|
|
R / Rfree (%)
|
14.5 /
16.5
|
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 ZINC001601221314 - (S) Isomer
(pdb code 5sq1). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the
Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC001601221314 - (S) Isomer, PDB code: 5sq1:
Jump to Fluorine binding site number:
1;
2;
Fluorine binding site 1 out
of 2 in 5sq1
Go back to
Fluorine Binding Sites List in 5sq1
Fluorine binding site 1 out
of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC001601221314 - (S) 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 ZINC001601221314 - (S) Isomer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:17.5
occ:0.38
|
F11
|
A:QJO201
|
0.0
|
17.5
|
0.4
|
|
O
|
A:HOH518
|
0.7
|
39.6
|
0.6
|
|
C10
|
A:QJO201
|
1.3
|
17.9
|
0.4
|
|
F17
|
A:QJO201
|
2.1
|
19.0
|
0.4
|
|
C09
|
A:QJO201
|
2.4
|
17.7
|
0.4
|
|
C12
|
A:QJO201
|
2.4
|
17.9
|
0.4
|
|
H092
|
A:QJO201
|
2.4
|
21.2
|
0.4
|
|
H121
|
A:QJO201
|
2.6
|
21.5
|
0.4
|
|
O
|
A:HOH423
|
2.7
|
21.4
|
0.6
|
|
HD23
|
A:LEU160
|
2.7
|
23.9
|
0.4
|
|
HB2
|
A:LEU126
|
2.7
|
17.3
|
0.4
|
|
HG13
|
A:VAL155
|
2.8
|
24.8
|
0.4
|
|
HD23
|
A:LEU160
|
2.9
|
27.2
|
0.6
|
|
HG13
|
A:VAL155
|
2.9
|
21.8
|
0.6
|
|
C13
|
A:QJO201
|
3.0
|
17.5
|
0.4
|
|
HD12
|
A:LEU126
|
3.1
|
20.8
|
0.4
|
|
HD12
|
A:LEU126
|
3.1
|
19.9
|
0.6
|
|
HD21
|
A:LEU160
|
3.1
|
27.2
|
0.6
|
|
O16
|
A:QJO201
|
3.1
|
17.4
|
0.4
|
|
H091
|
A:QJO201
|
3.2
|
21.2
|
0.4
|
|
C14
|
A:QJO201
|
3.2
|
17.5
|
0.4
|
|
N08
|
A:QJO201
|
3.2
|
17.5
|
0.4
|
|
O
|
A:HOH448
|
3.3
|
22.1
|
0.6
|
|
H122
|
A:QJO201
|
3.3
|
21.5
|
0.4
|
|
HB2
|
A:LEU126
|
3.3
|
16.1
|
0.6
|
|
O
|
A:HOH499
|
3.3
|
39.4
|
0.6
|
|
CD2
|
A:LEU160
|
3.4
|
22.7
|
0.6
|
|
O
|
A:HOH370
|
3.5
|
14.1
|
0.4
|
|
HD21
|
A:LEU160
|
3.5
|
23.9
|
0.4
|
|
CD2
|
A:LEU160
|
3.5
|
19.9
|
0.4
|
|
HB1
|
A:ALA129
|
3.5
|
17.3
|
0.6
|
|
O
|
A:HOH460
|
3.6
|
22.7
|
0.6
|
|
HG22
|
A:VAL155
|
3.6
|
21.0
|
0.6
|
|
HB3
|
A:ALA129
|
3.6
|
17.3
|
0.6
|
|
CB
|
A:LEU126
|
3.7
|
14.4
|
0.4
|
|
HG22
|
A:VAL155
|
3.7
|
24.5
|
0.4
|
|
CG1
|
A:VAL155
|
3.7
|
20.7
|
0.4
|
|
HA
|
A:VAL155
|
3.7
|
19.5
|
0.6
|
|
H
|
A:LEU126
|
3.8
|
15.4
|
0.4
|
|
CD1
|
A:LEU126
|
3.8
|
17.3
|
0.4
|
|
CG1
|
A:VAL155
|
3.8
|
18.2
|
0.6
|
|
HG11
|
A:VAL155
|
3.9
|
24.8
|
0.4
|
|
HD22
|
A:LEU160
|
3.9
|
27.2
|
0.6
|
|
HD13
|
A:LEU126
|
3.9
|
20.8
|
0.4
|
|
HB3
|
A:LEU126
|
3.9
|
17.3
|
0.4
|
|
O15
|
A:QJO201
|
4.0
|
18.1
|
0.4
|
|
CB
|
A:ALA129
|
4.0
|
14.4
|
0.6
|
|
CD1
|
A:LEU126
|
4.0
|
16.6
|
0.6
|
|
HD22
|
A:LEU160
|
4.0
|
23.9
|
0.4
|
|
HG11
|
A:VAL155
|
4.1
|
21.8
|
0.6
|
|
HB3
|
A:PRO136
|
4.1
|
20.7
|
0.6
|
|
H131
|
A:QJO201
|
4.1
|
21.0
|
0.4
|
|
HA
|
A:VAL155
|
4.1
|
23.3
|
0.4
|
|
H
|
A:LEU126
|
4.1
|
14.7
|
0.6
|
|
CB
|
A:LEU126
|
4.2
|
13.4
|
0.6
|
|
HB2
|
A:ALA129
|
4.3
|
17.3
|
0.6
|
|
CG
|
A:LEU126
|
4.3
|
16.2
|
0.4
|
|
H
|
A:PHE156
|
4.3
|
22.6
|
0.6
|
|
HG12
|
A:VAL155
|
4.3
|
24.8
|
0.4
|
|
HB3
|
A:ALA129
|
4.3
|
19.4
|
0.4
|
|
HD13
|
A:LEU126
|
4.4
|
19.9
|
0.6
|
|
CG2
|
A:VAL155
|
4.4
|
20.4
|
0.4
|
|
HG
|
A:LEU160
|
4.4
|
23.6
|
0.4
|
|
CG2
|
A:VAL155
|
4.4
|
17.5
|
0.6
|
|
HD11
|
A:LEU164
|
4.4
|
23.6
|
1.0
|
|
CB
|
A:VAL155
|
4.5
|
16.8
|
0.6
|
|
HG21
|
A:VAL155
|
4.5
|
24.5
|
0.4
|
|
O
|
A:HOH419
|
4.5
|
25.2
|
0.6
|
|
HG12
|
A:VAL155
|
4.5
|
21.8
|
0.6
|
|
CB
|
A:VAL155
|
4.5
|
20.0
|
0.4
|
|
N
|
A:LEU126
|
4.5
|
12.9
|
0.4
|
|
HG
|
A:LEU126
|
4.5
|
19.5
|
0.4
|
|
CA
|
A:VAL155
|
4.5
|
16.3
|
0.6
|
|
HG
|
A:LEU126
|
4.5
|
18.2
|
0.6
|
|
HG
|
A:LEU160
|
4.5
|
28.1
|
0.6
|
|
CG
|
A:LEU126
|
4.5
|
15.2
|
0.6
|
|
CG
|
A:LEU160
|
4.6
|
19.6
|
0.4
|
|
HD11
|
A:LEU126
|
4.6
|
19.9
|
0.6
|
|
HB3
|
A:PRO136
|
4.6
|
18.5
|
0.4
|
|
CG
|
A:LEU160
|
4.6
|
23.4
|
0.6
|
|
HD11
|
A:LEU126
|
4.6
|
20.8
|
0.4
|
|
CA
|
A:LEU126
|
4.7
|
12.8
|
0.4
|
|
HB2
|
A:PRO136
|
4.7
|
20.7
|
0.6
|
|
HB3
|
A:LEU126
|
4.7
|
16.1
|
0.6
|
|
HG21
|
A:VAL155
|
4.7
|
21.0
|
0.6
|
|
H
|
A:GLY130
|
4.8
|
15.5
|
0.6
|
|
S06
|
A:QJO201
|
4.8
|
17.6
|
0.4
|
|
CA
|
A:VAL155
|
4.8
|
19.4
|
0.4
|
|
O
|
A:LEU126
|
4.8
|
13.0
|
0.4
|
|
CB
|
A:PRO136
|
4.8
|
17.2
|
0.6
|
|
H
|
A:PHE156
|
4.8
|
23.7
|
0.4
|
|
O
|
A:HOH336
|
4.9
|
21.1
|
0.6
|
|
HB1
|
A:ALA129
|
4.9
|
19.4
|
0.4
|
|
N
|
A:LEU126
|
4.9
|
12.3
|
0.6
|
|
HB3
|
A:LEU160
|
4.9
|
22.9
|
0.4
|
|
N
|
A:PHE156
|
4.9
|
18.8
|
0.6
|
|
H
|
A:ASP157
|
5.0
|
26.8
|
0.6
|
|
Fluorine binding site 2 out
of 2 in 5sq1
Go back to
Fluorine Binding Sites List in 5sq1
Fluorine binding site 2 out
of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC001601221314 - (S) 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 ZINC001601221314 - (S) Isomer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:19.0
occ:0.38
|
F17
|
A:QJO201
|
0.0
|
19.0
|
0.4
|
|
C10
|
A:QJO201
|
1.3
|
17.9
|
0.4
|
|
HB1
|
A:ALA129
|
1.5
|
17.3
|
0.6
|
|
F11
|
A:QJO201
|
2.1
|
17.5
|
0.4
|
|
O
|
A:HOH518
|
2.2
|
39.6
|
0.6
|
|
CB
|
A:ALA129
|
2.2
|
14.4
|
0.6
|
|
HB3
|
A:ALA129
|
2.3
|
17.3
|
0.6
|
|
H091
|
A:QJO201
|
2.3
|
21.2
|
0.4
|
|
C09
|
A:QJO201
|
2.4
|
17.7
|
0.4
|
|
C12
|
A:QJO201
|
2.4
|
17.9
|
0.4
|
|
HB3
|
A:ALA129
|
2.5
|
19.4
|
0.4
|
|
H122
|
A:QJO201
|
2.6
|
21.5
|
0.4
|
|
HB2
|
A:ALA129
|
2.6
|
17.3
|
0.6
|
|
HB3
|
A:PRO136
|
2.8
|
20.7
|
0.6
|
|
HB1
|
A:ALA129
|
2.8
|
19.4
|
0.4
|
|
H092
|
A:QJO201
|
2.8
|
21.2
|
0.4
|
|
O
|
A:HOH419
|
2.8
|
25.2
|
0.6
|
|
H121
|
A:QJO201
|
2.9
|
21.5
|
0.4
|
|
H
|
A:GLY130
|
2.9
|
15.5
|
0.6
|
|
HD21
|
A:LEU160
|
3.0
|
23.9
|
0.4
|
|
CB
|
A:ALA129
|
3.1
|
16.2
|
0.4
|
|
HD21
|
A:LEU160
|
3.1
|
27.2
|
0.6
|
|
HB2
|
A:LEU126
|
3.1
|
17.3
|
0.4
|
|
HD23
|
A:LEU160
|
3.2
|
23.9
|
0.4
|
|
HB3
|
A:PRO136
|
3.3
|
18.5
|
0.4
|
|
H
|
A:GLY130
|
3.4
|
18.0
|
0.4
|
|
HB2
|
A:LEU126
|
3.4
|
16.1
|
0.6
|
|
N
|
A:GLY130
|
3.5
|
12.9
|
0.6
|
|
CD2
|
A:LEU160
|
3.5
|
19.9
|
0.4
|
|
CA
|
A:ALA129
|
3.5
|
12.9
|
0.6
|
|
HB3
|
A:LEU126
|
3.5
|
17.3
|
0.4
|
|
O
|
A:HOH499
|
3.6
|
39.4
|
0.6
|
|
N08
|
A:QJO201
|
3.6
|
17.5
|
0.4
|
|
HD23
|
A:LEU160
|
3.6
|
27.2
|
0.6
|
|
C13
|
A:QJO201
|
3.6
|
17.5
|
0.4
|
|
HB2
|
A:ALA129
|
3.6
|
19.4
|
0.4
|
|
CD2
|
A:LEU160
|
3.6
|
22.7
|
0.6
|
|
O
|
A:HOH342
|
3.7
|
25.3
|
0.4
|
|
CB
|
A:PRO136
|
3.7
|
17.2
|
0.6
|
|
HD22
|
A:LEU160
|
3.7
|
27.2
|
0.6
|
|
HD12
|
A:LEU126
|
3.7
|
19.9
|
0.6
|
|
CB
|
A:LEU126
|
3.8
|
14.4
|
0.4
|
|
HD22
|
A:LEU160
|
3.8
|
23.9
|
0.4
|
|
N
|
A:GLY130
|
3.8
|
15.0
|
0.4
|
|
HA
|
A:ALA129
|
3.8
|
15.5
|
0.6
|
|
C
|
A:ALA129
|
3.9
|
11.7
|
0.6
|
|
HG3
|
A:PRO136
|
4.0
|
21.7
|
0.6
|
|
HB2
|
A:PRO136
|
4.0
|
20.7
|
0.6
|
|
HD12
|
A:LEU126
|
4.0
|
20.8
|
0.4
|
|
HD13
|
A:LEU126
|
4.0
|
20.8
|
0.4
|
|
O
|
A:LEU126
|
4.1
|
13.0
|
0.4
|
|
O
|
A:HOH423
|
4.2
|
21.4
|
0.6
|
|
CA
|
A:ALA129
|
4.2
|
14.2
|
0.4
|
|
C
|
A:ALA129
|
4.2
|
15.2
|
0.4
|
|
CB
|
A:PRO136
|
4.3
|
15.4
|
0.4
|
|
CB
|
A:LEU126
|
4.3
|
13.4
|
0.6
|
|
HB3
|
A:LEU126
|
4.3
|
16.1
|
0.6
|
|
HD13
|
A:LEU126
|
4.4
|
19.9
|
0.6
|
|
H131
|
A:QJO201
|
4.4
|
21.0
|
0.4
|
|
CG
|
A:PRO136
|
4.4
|
18.1
|
0.6
|
|
CD1
|
A:LEU126
|
4.4
|
17.3
|
0.4
|
|
HA
|
A:PRO136
|
4.4
|
19.9
|
0.6
|
|
CA
|
A:GLY130
|
4.5
|
13.9
|
0.6
|
|
HA2
|
A:GLY130
|
4.5
|
16.7
|
0.6
|
|
CD1
|
A:LEU126
|
4.5
|
16.6
|
0.6
|
|
O
|
A:HOH448
|
4.5
|
22.1
|
0.6
|
|
HA3
|
A:GLY130
|
4.5
|
18.5
|
0.4
|
|
C14
|
A:QJO201
|
4.5
|
17.5
|
0.4
|
|
O
|
A:HOH336
|
4.5
|
21.1
|
0.6
|
|
HA3
|
A:GLY130
|
4.6
|
16.7
|
0.6
|
|
H
|
A:ALA129
|
4.6
|
13.9
|
0.6
|
|
H
|
A:LEU126
|
4.6
|
15.4
|
0.4
|
|
HB2
|
A:PRO136
|
4.6
|
18.5
|
0.4
|
|
HA2
|
A:GLY130
|
4.6
|
18.5
|
0.4
|
|
CA
|
A:GLY130
|
4.6
|
15.4
|
0.4
|
|
HG3
|
A:PRO136
|
4.6
|
19.2
|
0.4
|
|
O
|
A:LEU126
|
4.6
|
12.8
|
0.6
|
|
N
|
A:ALA129
|
4.6
|
11.6
|
0.6
|
|
H
|
A:ALA129
|
4.7
|
14.3
|
0.4
|
|
CA
|
A:PRO136
|
4.7
|
16.6
|
0.6
|
|
HD3
|
A:PRO136
|
4.7
|
21.3
|
0.6
|
|
CG
|
A:LEU126
|
4.7
|
16.2
|
0.4
|
|
HG13
|
A:VAL155
|
4.8
|
24.8
|
0.4
|
|
O16
|
A:QJO201
|
4.8
|
17.4
|
0.4
|
|
HA
|
A:PRO136
|
4.8
|
17.5
|
0.4
|
|
CA
|
A:LEU126
|
4.8
|
12.8
|
0.4
|
|
HG13
|
A:VAL155
|
4.8
|
21.8
|
0.6
|
|
C
|
A:LEU126
|
4.8
|
12.3
|
0.4
|
|
S06
|
A:QJO201
|
4.8
|
17.6
|
0.4
|
|
CG
|
A:LEU160
|
4.9
|
19.6
|
0.4
|
|
HA
|
A:ALA129
|
4.9
|
17.1
|
0.4
|
|
HG
|
A:LEU160
|
4.9
|
23.6
|
0.4
|
|
H
|
A:LEU126
|
4.9
|
14.7
|
0.6
|
|
O
|
A:HOH460
|
5.0
|
22.7
|
0.6
|
|
O
|
A:ALA129
|
5.0
|
11.8
|
0.6
|
|
O
|
A:HOH370
|
5.0
|
14.1
|
0.4
|
|
O
|
A:HOH472
|
5.0
|
51.9
|
1.0
|
|
Reference:
S.Gahbauer,
G.J.Correy,
M.Schuller,
M.P.Ferla,
Y.U.Doruk,
M.Rachman,
T.Wu,
M.Diolaiti,
S.Wang,
R.J.Neitz,
D.Fearon,
D.Radchenko,
Y.Moroz,
J.J.Irwin,
A.R.Renslo,
J.C.Taylor,
J.E.Gestwicki,
F.Von Delft,
A.Ashworth,
I.Ahel,
B.K.Shoichet,
J.S.Fraser.
Structure-Based Inhibitor Optimization For the NSP3 Macrodomain of Sars-Cov-2. Biorxiv 2022.
ISSN: ISSN 2692-8205
PubMed: 35794891
DOI: 10.1101/2022.06.27.497816
Page generated: Tue Apr 4 23:51:18 2023
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