Fluorine in PDB 4weg: Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid
Enzymatic activity of Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid
All present enzymatic activity of Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid:
3.2.1.18;
Protein crystallography data
The structure of Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid, PDB code: 4weg
was solved by
V.A.Streltsov,
P.Pilling,
S.Barrett,
J.Mckimm-Breschkin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.71 /
2.10
|
Space group
|
I 4 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.194,
181.194,
181.194,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.3 /
20.1
|
Other elements in 4weg:
The structure of Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid
(pdb code 4weg). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid, PDB code: 4weg:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 4weg
Go back to
Fluorine Binding Sites List in 4weg
Fluorine binding site 1 out
of 4 in the Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid
![](/pictures/F/pdb/we/4weg-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/we/4weg-F-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:72.0
occ:1.00
|
FAI
|
A:SFJ501
|
0.0
|
72.0
|
1.0
|
CAS
|
A:SFJ501
|
1.4
|
70.8
|
1.0
|
CAV
|
A:SFJ501
|
2.4
|
70.7
|
1.0
|
CAR
|
A:SFJ501
|
2.4
|
58.4
|
1.0
|
OAH
|
A:SFJ501
|
2.5
|
56.6
|
1.0
|
FAJ
|
A:SFJ501
|
2.6
|
72.8
|
1.0
|
O
|
A:HOH734
|
2.9
|
59.7
|
1.0
|
OAM
|
A:SFJ501
|
2.9
|
66.4
|
1.0
|
CAT
|
A:SFJ501
|
3.2
|
63.5
|
1.0
|
O
|
A:HOH909
|
3.4
|
57.0
|
1.0
|
CAU
|
A:SFJ501
|
3.7
|
67.0
|
1.0
|
CAO
|
A:SFJ501
|
3.8
|
66.4
|
1.0
|
OAE
|
A:SFJ501
|
4.1
|
63.0
|
1.0
|
NAL
|
A:SFJ501
|
4.5
|
51.5
|
1.0
|
OAG
|
A:SFJ501
|
4.6
|
53.8
|
1.0
|
CAQ
|
A:SFJ501
|
4.8
|
63.4
|
1.0
|
OAC
|
A:SFJ501
|
4.8
|
55.8
|
1.0
|
OD1
|
A:ASN399
|
4.9
|
43.5
|
1.0
|
OAB
|
A:SFJ501
|
5.0
|
51.5
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 4weg
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Fluorine Binding Sites List in 4weg
Fluorine binding site 2 out
of 4 in the Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid
![](/pictures/F/pdb/we/4weg-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/we/4weg-F-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:72.8
occ:1.00
|
FAJ
|
A:SFJ501
|
0.0
|
72.8
|
1.0
|
CAV
|
A:SFJ501
|
1.3
|
70.7
|
1.0
|
OAM
|
A:SFJ501
|
2.2
|
66.4
|
1.0
|
CAO
|
A:SFJ501
|
2.3
|
66.4
|
1.0
|
CAS
|
A:SFJ501
|
2.4
|
70.8
|
1.0
|
FAI
|
A:SFJ501
|
2.6
|
72.0
|
1.0
|
OAC
|
A:SFJ501
|
3.1
|
55.8
|
1.0
|
OAE
|
A:SFJ501
|
3.1
|
63.0
|
1.0
|
CAU
|
A:SFJ501
|
3.5
|
67.0
|
1.0
|
CAR
|
A:SFJ501
|
3.7
|
58.4
|
1.0
|
CAT
|
A:SFJ501
|
4.1
|
63.5
|
1.0
|
OAF
|
A:SFJ501
|
4.3
|
70.8
|
1.0
|
CAQ
|
A:SFJ501
|
4.5
|
63.4
|
1.0
|
CAP
|
A:SFJ501
|
4.6
|
68.3
|
1.0
|
OAG
|
A:SFJ501
|
4.6
|
53.8
|
1.0
|
OAH
|
A:SFJ501
|
4.6
|
56.6
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 4weg
Go back to
Fluorine Binding Sites List in 4weg
Fluorine binding site 3 out
of 4 in the Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid
![](/pictures/F/pdb/we/4weg-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/we/4weg-F-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F514
b:57.7
occ:0.70
|
F1
|
A:DF4514
|
0.0
|
57.7
|
0.7
|
C3
|
A:DF4514
|
1.4
|
39.5
|
0.7
|
C3
|
A:FSI515
|
1.4
|
25.0
|
0.3
|
F1
|
A:FSI515
|
1.6
|
24.5
|
0.3
|
C4
|
A:FSI515
|
2.1
|
24.8
|
0.3
|
O4
|
A:FSI515
|
2.1
|
23.6
|
0.3
|
C4
|
A:DF4514
|
2.4
|
37.4
|
0.7
|
C2
|
A:DF4514
|
2.4
|
35.0
|
0.7
|
O4
|
A:DF4514
|
2.5
|
34.1
|
0.7
|
OE2
|
A:GLU119
|
2.5
|
25.2
|
1.0
|
C2
|
A:FSI515
|
2.8
|
25.9
|
0.3
|
O1A
|
A:DF4514
|
2.9
|
28.9
|
0.7
|
C1
|
A:DF4514
|
3.0
|
32.0
|
0.7
|
O1B
|
A:FSI515
|
3.0
|
24.8
|
0.3
|
NH1
|
A:ARG118
|
3.1
|
30.1
|
1.0
|
OD1
|
A:ASP151
|
3.2
|
30.9
|
1.0
|
C1
|
A:FSI515
|
3.2
|
25.0
|
0.3
|
O
|
A:HOH610
|
3.3
|
28.7
|
1.0
|
C5
|
A:FSI515
|
3.3
|
23.9
|
0.3
|
O6
|
A:DF4514
|
3.4
|
34.8
|
0.7
|
C5
|
A:DF4514
|
3.4
|
32.8
|
0.7
|
CD
|
A:GLU119
|
3.6
|
27.3
|
1.0
|
O6
|
A:FSI515
|
3.6
|
25.5
|
0.3
|
CG
|
A:ASP151
|
3.7
|
35.6
|
1.0
|
CZ
|
A:ARG118
|
3.7
|
29.2
|
1.0
|
OH
|
A:TYR405
|
3.8
|
28.0
|
1.0
|
O
|
A:HOH833
|
3.8
|
53.4
|
1.0
|
NH2
|
A:ARG118
|
3.9
|
24.9
|
1.0
|
C6
|
A:DF4514
|
3.9
|
33.6
|
0.7
|
C6
|
A:FSI515
|
4.0
|
24.8
|
0.3
|
OD2
|
A:ASP151
|
4.2
|
36.0
|
1.0
|
O1B
|
A:DF4514
|
4.2
|
30.2
|
0.7
|
CG
|
A:GLU119
|
4.2
|
24.8
|
1.0
|
CZ
|
A:TYR405
|
4.3
|
27.3
|
1.0
|
O1A
|
A:FSI515
|
4.4
|
23.1
|
0.3
|
O
|
A:HOH751
|
4.4
|
29.5
|
1.0
|
N5
|
A:FSI515
|
4.5
|
24.1
|
0.3
|
CB
|
A:ASP151
|
4.5
|
32.7
|
1.0
|
OE1
|
A:GLU119
|
4.6
|
27.9
|
1.0
|
N5
|
A:DF4514
|
4.6
|
32.4
|
0.7
|
CE2
|
A:TYR405
|
4.7
|
23.5
|
1.0
|
O
|
A:HOH629
|
4.7
|
31.4
|
1.0
|
NE
|
A:ARG118
|
4.7
|
26.1
|
1.0
|
O
|
A:HOH868
|
4.8
|
25.9
|
1.0
|
O
|
A:HOH674
|
5.0
|
32.9
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 4weg
Go back to
Fluorine Binding Sites List in 4weg
Fluorine binding site 4 out
of 4 in the Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid
![](/pictures/F/pdb/we/4weg-F-sphere_04.jpg) Mono view
![](/pictures/F/pdb/we/4weg-F-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Influenza Virus Neuraminidase N9 in Complex 2,3-Difluorosialic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F515
b:24.5
occ:0.30
|
F1
|
A:FSI515
|
0.0
|
24.5
|
0.3
|
C2
|
A:DF4514
|
1.3
|
35.0
|
0.7
|
C3
|
A:FSI515
|
1.4
|
25.0
|
0.3
|
C3
|
A:DF4514
|
1.6
|
39.5
|
0.7
|
F1
|
A:DF4514
|
1.6
|
57.7
|
0.7
|
C1
|
A:DF4514
|
2.0
|
32.0
|
0.7
|
O6
|
A:DF4514
|
2.2
|
34.8
|
0.7
|
C2
|
A:FSI515
|
2.3
|
25.9
|
0.3
|
C4
|
A:FSI515
|
2.3
|
24.8
|
0.3
|
C1
|
A:FSI515
|
2.5
|
25.0
|
0.3
|
O1A
|
A:DF4514
|
2.6
|
28.9
|
0.7
|
O6
|
A:FSI515
|
2.6
|
25.5
|
0.3
|
C4
|
A:DF4514
|
2.6
|
37.4
|
0.7
|
O1B
|
A:FSI515
|
2.7
|
24.8
|
0.3
|
O4
|
A:FSI515
|
2.7
|
23.6
|
0.3
|
O
|
A:HOH751
|
2.8
|
29.5
|
1.0
|
C5
|
A:FSI515
|
2.9
|
23.9
|
0.3
|
C5
|
A:DF4514
|
3.0
|
32.8
|
0.7
|
O1B
|
A:DF4514
|
3.0
|
30.2
|
0.7
|
C6
|
A:DF4514
|
3.0
|
33.6
|
0.7
|
O
|
A:HOH833
|
3.1
|
53.4
|
1.0
|
C6
|
A:FSI515
|
3.2
|
24.8
|
0.3
|
O4
|
A:DF4514
|
3.2
|
34.1
|
0.7
|
O1A
|
A:FSI515
|
3.3
|
23.1
|
0.3
|
OD1
|
A:ASP151
|
3.4
|
30.9
|
1.0
|
OD2
|
A:ASP151
|
3.5
|
36.0
|
1.0
|
CG
|
A:ASP151
|
3.6
|
35.6
|
1.0
|
OH
|
A:TYR405
|
3.7
|
28.0
|
1.0
|
NH1
|
A:ARG118
|
3.9
|
30.1
|
1.0
|
O7
|
A:FSI515
|
3.9
|
25.6
|
0.3
|
O7
|
A:DF4514
|
4.1
|
36.0
|
0.7
|
C7
|
A:FSI515
|
4.1
|
24.2
|
0.3
|
OE2
|
A:GLU119
|
4.2
|
25.2
|
1.0
|
C7
|
A:DF4514
|
4.2
|
32.9
|
0.7
|
N5
|
A:FSI515
|
4.3
|
24.1
|
0.3
|
N5
|
A:DF4514
|
4.4
|
32.4
|
0.7
|
O
|
A:HOH968
|
4.4
|
47.9
|
1.0
|
O
|
A:HOH629
|
4.4
|
31.4
|
1.0
|
O
|
A:HOH807
|
4.5
|
52.4
|
1.0
|
CZ
|
A:TYR405
|
4.5
|
27.3
|
1.0
|
O
|
A:HOH610
|
4.6
|
28.7
|
1.0
|
CB
|
A:ASP151
|
4.6
|
32.7
|
1.0
|
CZ
|
A:ARG118
|
4.7
|
29.2
|
1.0
|
NH2
|
A:ARG118
|
4.8
|
24.9
|
1.0
|
C8
|
A:FSI515
|
4.9
|
24.2
|
0.3
|
|
Reference:
V.A.Streltsov,
P.Pilling,
S.Barrett,
J.L.Mckimm-Breschkin.
Catalytic Mechanism and Novel Receptor Binding Sites of Human Parainfluenza Virus Type 3 Hemagglutinin-Neuraminidase (HPIV3 Hn) Antiviral Res. V. 123 216 2015.
ISSN: ISSN 0166-3542
PubMed: 26364554
DOI: 10.1016/J.ANTIVIRAL.2015.08.014
Page generated: Thu Aug 1 06:19:35 2024
|