Fluorine in PDB 5we9: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)
Protein crystallography data
The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731), PDB code: 5we9
was solved by
G.Kumar,
S.W.White,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.57 /
1.80
|
Space group
|
P 64 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.081,
74.081,
127.694,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19 /
22.6
|
Other elements in 5we9:
The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)
(pdb code 5we9). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731), PDB code: 5we9:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 5we9
Go back to
Fluorine Binding Sites List in 5we9
Fluorine binding site 1 out
of 4 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)
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 the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F303
b:32.7
occ:0.44
|
F1
|
A:GY7303
|
0.0
|
32.7
|
0.4
|
C1
|
A:GY7303
|
1.4
|
27.4
|
0.4
|
F2
|
A:GY7303
|
1.7
|
33.2
|
0.6
|
O1
|
A:GY7303
|
2.0
|
23.3
|
0.6
|
C3
|
A:GY7303
|
2.1
|
21.4
|
0.6
|
C21
|
A:GY7303
|
2.2
|
22.2
|
0.6
|
C24
|
A:GY7303
|
2.3
|
25.7
|
0.4
|
C2
|
A:GY7303
|
2.4
|
27.2
|
0.6
|
C2
|
A:GY7303
|
2.4
|
25.1
|
0.4
|
C3
|
A:GY7303
|
2.9
|
23.0
|
0.4
|
N1
|
A:GY7303
|
2.9
|
24.2
|
0.6
|
N2
|
A:GY7303
|
3.0
|
8.6
|
0.6
|
O1
|
A:GY7303
|
3.1
|
26.1
|
0.4
|
N3
|
A:GY7303
|
3.2
|
17.3
|
0.6
|
C22
|
A:GY7303
|
3.5
|
14.7
|
0.6
|
N3
|
A:GY7303
|
3.5
|
15.2
|
0.4
|
N2
|
A:GY7303
|
3.6
|
9.2
|
0.4
|
C23
|
A:GY7303
|
3.6
|
17.4
|
0.4
|
C21
|
A:GY7303
|
3.6
|
27.5
|
0.4
|
C5
|
A:GY7303
|
3.6
|
13.5
|
0.6
|
C6
|
A:GY7303
|
3.6
|
9.7
|
0.6
|
C1
|
A:GY7303
|
3.7
|
30.8
|
0.6
|
N1
|
A:GY7303
|
3.7
|
25.4
|
0.4
|
C7
|
A:GY7303
|
3.8
|
13.5
|
0.6
|
C4
|
A:GY7303
|
3.8
|
19.9
|
0.6
|
C20
|
A:GY7303
|
3.9
|
26.4
|
0.6
|
C6
|
A:GY7303
|
4.0
|
7.6
|
0.4
|
C7
|
A:GY7303
|
4.0
|
14.2
|
0.4
|
C8
|
A:GY7303
|
4.0
|
24.6
|
0.4
|
C8
|
A:GY7303
|
4.1
|
24.5
|
0.6
|
C22
|
A:GY7303
|
4.1
|
30.1
|
0.4
|
O
|
A:HOH496
|
4.2
|
33.1
|
1.0
|
C5
|
A:GY7303
|
4.2
|
12.3
|
0.4
|
F1
|
A:GY7303
|
4.4
|
29.5
|
0.6
|
C23
|
A:GY7303
|
4.5
|
25.5
|
0.6
|
C20
|
A:GY7303
|
4.5
|
29.1
|
0.4
|
C4
|
A:GY7303
|
4.5
|
20.3
|
0.4
|
C24
|
A:GY7303
|
4.6
|
27.0
|
0.6
|
C15
|
A:GY7303
|
4.6
|
41.9
|
0.6
|
CG1
|
A:ILE38
|
4.7
|
11.5
|
1.0
|
N4
|
A:GY7303
|
4.7
|
11.8
|
0.6
|
F2
|
A:GY7303
|
4.7
|
34.4
|
0.4
|
C16
|
A:GY7303
|
4.7
|
9.7
|
0.6
|
C10
|
A:GY7303
|
4.8
|
39.5
|
0.6
|
C19
|
A:GY7303
|
4.8
|
26.9
|
0.6
|
O2
|
A:GY7303
|
4.8
|
14.1
|
0.6
|
C15
|
A:GY7303
|
4.8
|
42.0
|
0.4
|
O
|
A:HOH416
|
4.9
|
21.6
|
1.0
|
C16
|
A:GY7303
|
4.9
|
9.2
|
0.4
|
O2
|
A:GY7303
|
4.9
|
10.5
|
0.4
|
C14
|
A:GY7303
|
4.9
|
42.4
|
0.6
|
CD1
|
A:ILE38
|
5.0
|
14.8
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 5we9
Go back to
Fluorine Binding Sites List in 5we9
Fluorine binding site 2 out
of 4 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)
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 the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F303
b:29.5
occ:0.56
|
F1
|
A:GY7303
|
0.0
|
29.5
|
0.6
|
C1
|
A:GY7303
|
1.4
|
30.8
|
0.6
|
O1
|
A:GY7303
|
2.2
|
26.1
|
0.4
|
C24
|
A:GY7303
|
2.3
|
27.0
|
0.6
|
C2
|
A:GY7303
|
2.4
|
27.2
|
0.6
|
C3
|
A:GY7303
|
2.8
|
21.4
|
0.6
|
C3
|
A:GY7303
|
3.2
|
23.0
|
0.4
|
CD
|
A:LYS34
|
3.4
|
40.7
|
1.0
|
O1
|
A:GY7303
|
3.4
|
23.3
|
0.6
|
CG
|
A:LYS34
|
3.4
|
34.9
|
1.0
|
N1
|
A:GY7303
|
3.5
|
24.2
|
0.6
|
CD1
|
A:ILE38
|
3.5
|
14.8
|
1.0
|
C23
|
A:GY7303
|
3.6
|
25.5
|
0.6
|
C21
|
A:GY7303
|
3.6
|
22.2
|
0.6
|
C2
|
A:GY7303
|
3.7
|
25.1
|
0.4
|
CG1
|
A:ILE38
|
3.8
|
11.5
|
1.0
|
C20
|
A:GY7303
|
3.9
|
26.4
|
0.6
|
C22
|
A:GY7303
|
4.1
|
14.7
|
0.6
|
C21
|
A:GY7303
|
4.3
|
27.5
|
0.4
|
N1
|
A:GY7303
|
4.3
|
25.4
|
0.4
|
C1
|
A:GY7303
|
4.3
|
27.4
|
0.4
|
F2
|
A:GY7303
|
4.4
|
34.4
|
0.4
|
F1
|
A:GY7303
|
4.4
|
32.7
|
0.4
|
CE
|
A:LYS34
|
4.5
|
40.7
|
1.0
|
C4
|
A:GY7303
|
4.6
|
19.9
|
0.6
|
OE2
|
A:GLU26
|
4.6
|
43.1
|
1.0
|
F2
|
A:GY7303
|
4.7
|
33.2
|
0.6
|
C20
|
A:GY7303
|
4.9
|
29.1
|
0.4
|
CB
|
A:LYS34
|
4.9
|
20.6
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 5we9
Go back to
Fluorine Binding Sites List in 5we9
Fluorine binding site 3 out
of 4 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)
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 the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F303
b:34.4
occ:0.44
|
F2
|
A:GY7303
|
0.0
|
34.4
|
0.4
|
C21
|
A:GY7303
|
1.4
|
27.5
|
0.4
|
C4
|
A:GY7303
|
2.0
|
19.9
|
0.6
|
C22
|
A:GY7303
|
2.3
|
30.1
|
0.4
|
C2
|
A:GY7303
|
2.4
|
25.1
|
0.4
|
N1
|
A:GY7303
|
2.8
|
24.2
|
0.6
|
C3
|
A:GY7303
|
2.8
|
23.0
|
0.4
|
C18
|
A:GY7303
|
2.9
|
27.5
|
0.6
|
C5
|
A:GY7303
|
2.9
|
13.5
|
0.6
|
O1
|
A:GY7303
|
3.0
|
23.3
|
0.6
|
C4
|
A:GY7303
|
3.0
|
20.3
|
0.4
|
C3
|
A:GY7303
|
3.2
|
21.4
|
0.6
|
N1
|
A:GY7303
|
3.2
|
25.4
|
0.4
|
N4
|
A:GY7303
|
3.2
|
11.8
|
0.6
|
O
|
A:HOH500
|
3.5
|
32.2
|
1.0
|
C5
|
A:GY7303
|
3.6
|
12.3
|
0.4
|
C23
|
A:GY7303
|
3.6
|
17.4
|
0.4
|
C1
|
A:GY7303
|
3.6
|
27.4
|
0.4
|
O1
|
A:GY7303
|
3.6
|
26.1
|
0.4
|
N4
|
A:GY7303
|
3.7
|
9.2
|
0.4
|
C20
|
A:GY7303
|
3.9
|
26.4
|
0.6
|
N2
|
A:GY7303
|
4.0
|
8.6
|
0.6
|
C19
|
A:GY7303
|
4.1
|
26.9
|
0.6
|
C24
|
A:GY7303
|
4.1
|
25.7
|
0.4
|
O
|
A:HOH445
|
4.2
|
30.3
|
1.0
|
C18
|
A:GY7303
|
4.3
|
27.4
|
0.4
|
F1
|
A:GY7303
|
4.4
|
29.5
|
0.6
|
N2
|
A:GY7303
|
4.5
|
9.2
|
0.4
|
C17
|
A:GY7303
|
4.5
|
12.6
|
0.6
|
C2
|
A:GY7303
|
4.5
|
27.2
|
0.6
|
C20
|
A:GY7303
|
4.6
|
29.1
|
0.4
|
O
|
A:HOH415
|
4.6
|
14.9
|
1.0
|
F1
|
A:GY7303
|
4.7
|
32.7
|
0.4
|
OH
|
A:TYR130
|
4.7
|
41.5
|
1.0
|
C17
|
A:GY7303
|
4.8
|
10.9
|
0.4
|
NH2
|
A:ARG124
|
4.9
|
38.1
|
1.0
|
C1
|
A:GY7303
|
5.0
|
30.8
|
0.6
|
|
Fluorine binding site 4 out
of 4 in 5we9
Go back to
Fluorine Binding Sites List in 5we9
Fluorine binding site 4 out
of 4 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)
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 the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F303
b:33.2
occ:0.56
|
F2
|
A:GY7303
|
0.0
|
33.2
|
0.6
|
C21
|
A:GY7303
|
1.4
|
22.2
|
0.6
|
F1
|
A:GY7303
|
1.7
|
32.7
|
0.4
|
C22
|
A:GY7303
|
2.3
|
14.7
|
0.6
|
C2
|
A:GY7303
|
2.4
|
27.2
|
0.6
|
C3
|
A:GY7303
|
2.8
|
21.4
|
0.6
|
C1
|
A:GY7303
|
3.0
|
27.4
|
0.4
|
C15
|
A:GY7303
|
3.0
|
41.9
|
0.6
|
N3
|
A:GY7303
|
3.0
|
17.3
|
0.6
|
N3
|
A:GY7303
|
3.2
|
15.2
|
0.4
|
O1
|
A:GY7303
|
3.3
|
26.1
|
0.4
|
C15
|
A:GY7303
|
3.3
|
42.0
|
0.4
|
C8
|
A:GY7303
|
3.3
|
24.6
|
0.4
|
C3
|
A:GY7303
|
3.4
|
23.0
|
0.4
|
C8
|
A:GY7303
|
3.4
|
24.5
|
0.6
|
C14
|
A:GY7303
|
3.4
|
42.4
|
0.6
|
O1
|
A:GY7303
|
3.4
|
23.3
|
0.6
|
N1
|
A:GY7303
|
3.4
|
24.2
|
0.6
|
C10
|
A:GY7303
|
3.5
|
39.5
|
0.6
|
C2
|
A:GY7303
|
3.6
|
25.1
|
0.4
|
C23
|
A:GY7303
|
3.6
|
25.5
|
0.6
|
C1
|
A:GY7303
|
3.6
|
30.8
|
0.6
|
C20
|
A:GY7303
|
3.7
|
26.4
|
0.6
|
N2
|
A:GY7303
|
3.7
|
8.6
|
0.6
|
C10
|
A:GY7303
|
3.8
|
39.4
|
0.4
|
C14
|
A:GY7303
|
3.8
|
42.0
|
0.4
|
N1
|
A:GY7303
|
3.9
|
25.4
|
0.4
|
C9
|
A:GY7303
|
4.0
|
33.1
|
0.6
|
C24
|
A:GY7303
|
4.0
|
25.7
|
0.4
|
C9
|
A:GY7303
|
4.1
|
32.9
|
0.4
|
N2
|
A:GY7303
|
4.1
|
9.2
|
0.4
|
C7
|
A:GY7303
|
4.1
|
13.5
|
0.6
|
C24
|
A:GY7303
|
4.1
|
27.0
|
0.6
|
C20
|
A:GY7303
|
4.1
|
29.1
|
0.4
|
C13
|
A:GY7303
|
4.2
|
42.8
|
0.6
|
C7
|
A:GY7303
|
4.2
|
14.2
|
0.4
|
C11
|
A:GY7303
|
4.3
|
38.8
|
0.6
|
C6
|
A:GY7303
|
4.4
|
9.7
|
0.6
|
C12
|
A:GY7303
|
4.6
|
39.2
|
0.6
|
C6
|
A:GY7303
|
4.6
|
7.6
|
0.4
|
C4
|
A:GY7303
|
4.6
|
19.9
|
0.6
|
C5
|
A:GY7303
|
4.6
|
13.5
|
0.6
|
C11
|
A:GY7303
|
4.6
|
37.5
|
0.4
|
O
|
A:HOH518
|
4.6
|
44.2
|
1.0
|
C13
|
A:GY7303
|
4.7
|
40.7
|
0.4
|
F1
|
A:GY7303
|
4.7
|
29.5
|
0.6
|
C19
|
A:GY7303
|
4.7
|
26.9
|
0.6
|
C5
|
A:GY7303
|
4.9
|
12.3
|
0.4
|
C21
|
A:GY7303
|
5.0
|
27.5
|
0.4
|
|
Reference:
D.Beylkin,
G.Kumar,
W.Zhou,
J.Park,
T.Jeevan,
C.Lagisetti,
R.Harfoot,
R.J.Webby,
S.W.White,
T.R.Webb.
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ISSN: ESSN 2045-2322
PubMed: 29215062
DOI: 10.1038/S41598-017-17419-6
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