Fluorine in PDB 5jb2: Crystal Structure of Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution.
Protein crystallography data
The structure of Crystal Structure of Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution., PDB code: 5jb2
was solved by
S.Cusack,
E.Uchikawa,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
75.93 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.140,
96.580,
122.860,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.8 /
24.5
|
Other elements in 5jb2:
The structure of Crystal Structure of Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution. also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution.
(pdb code 5jb2). 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 Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution., PDB code: 5jb2:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 5jb2
Go back to
Fluorine Binding Sites List in 5jb2
Fluorine binding site 1 out
of 4 in the Crystal Structure of Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution.
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 Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F703
b:19.1
occ:1.00
|
F1
|
A:ALF703
|
0.0
|
19.1
|
1.0
|
AL
|
A:ALF703
|
1.8
|
18.5
|
1.0
|
MG
|
A:MG704
|
1.9
|
17.7
|
1.0
|
F3
|
A:ALF703
|
2.5
|
18.1
|
1.0
|
F4
|
A:ALF703
|
2.6
|
19.6
|
1.0
|
O
|
A:HOH817
|
2.7
|
17.5
|
1.0
|
O
|
A:HOH988
|
2.7
|
30.2
|
1.0
|
O3B
|
A:ADP702
|
2.8
|
16.1
|
1.0
|
O2B
|
A:ADP702
|
2.8
|
15.6
|
1.0
|
O
|
A:HOH819
|
3.0
|
15.7
|
1.0
|
OE2
|
A:GLU132
|
3.2
|
17.0
|
1.0
|
PB
|
A:ADP702
|
3.2
|
17.1
|
1.0
|
O
|
A:HOH828
|
3.4
|
16.9
|
1.0
|
O
|
A:HOH852
|
3.4
|
17.0
|
1.0
|
CE
|
A:LYS30
|
3.5
|
18.0
|
1.0
|
F2
|
A:ALF703
|
3.6
|
17.2
|
1.0
|
O
|
A:HOH934
|
3.8
|
17.2
|
1.0
|
NZ
|
A:LYS30
|
3.8
|
18.3
|
1.0
|
CD
|
A:GLU132
|
3.9
|
17.2
|
1.0
|
O1B
|
A:ADP702
|
4.0
|
16.4
|
1.0
|
OE1
|
A:GLU132
|
4.1
|
17.7
|
1.0
|
OD1
|
A:ASP131
|
4.5
|
17.5
|
1.0
|
O3A
|
A:ADP702
|
4.6
|
17.1
|
1.0
|
CA
|
A:GLY442
|
4.6
|
18.7
|
1.0
|
CD
|
A:LYS30
|
4.8
|
18.5
|
1.0
|
N
|
A:GLY442
|
4.9
|
18.8
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 5jb2
Go back to
Fluorine Binding Sites List in 5jb2
Fluorine binding site 2 out
of 4 in the Crystal Structure of Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution.
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 Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F703
b:17.2
occ:1.00
|
F2
|
A:ALF703
|
0.0
|
17.2
|
1.0
|
AL
|
A:ALF703
|
1.8
|
18.5
|
1.0
|
F4
|
A:ALF703
|
2.5
|
19.6
|
1.0
|
O2B
|
A:ADP702
|
2.5
|
15.6
|
1.0
|
F3
|
A:ALF703
|
2.6
|
18.1
|
1.0
|
O
|
A:HOH817
|
2.6
|
17.5
|
1.0
|
NH1
|
A:ARG471
|
2.8
|
21.8
|
1.0
|
NH2
|
A:ARG469
|
2.9
|
15.2
|
1.0
|
NH1
|
A:ARG469
|
3.2
|
15.9
|
1.0
|
N
|
A:GLY27
|
3.3
|
19.4
|
1.0
|
CA
|
A:THR26
|
3.4
|
18.7
|
1.0
|
NH2
|
A:ARG471
|
3.5
|
20.8
|
1.0
|
CB
|
A:THR26
|
3.5
|
18.0
|
1.0
|
CZ
|
A:ARG469
|
3.5
|
15.4
|
1.0
|
CZ
|
A:ARG471
|
3.6
|
21.2
|
1.0
|
F1
|
A:ALF703
|
3.6
|
19.1
|
1.0
|
C
|
A:THR26
|
3.8
|
19.4
|
1.0
|
CG2
|
A:THR26
|
3.8
|
17.9
|
1.0
|
PB
|
A:ADP702
|
4.0
|
17.1
|
1.0
|
OE1
|
A:GLN465
|
4.1
|
19.6
|
1.0
|
CA
|
A:GLY27
|
4.4
|
20.1
|
1.0
|
MG
|
A:MG704
|
4.4
|
17.7
|
1.0
|
N
|
A:GLY442
|
4.6
|
18.8
|
1.0
|
O3A
|
A:ADP702
|
4.7
|
17.1
|
1.0
|
O3B
|
A:ADP702
|
4.7
|
16.1
|
1.0
|
OG1
|
A:THR26
|
4.8
|
17.0
|
1.0
|
N
|
A:THR26
|
4.8
|
20.0
|
1.0
|
NE
|
A:ARG469
|
4.8
|
15.6
|
1.0
|
NZ
|
A:LYS30
|
4.8
|
18.3
|
1.0
|
O
|
A:HOH852
|
4.8
|
17.0
|
1.0
|
NE
|
A:ARG471
|
4.9
|
21.0
|
1.0
|
CA
|
A:GLY442
|
4.9
|
18.7
|
1.0
|
O
|
A:THR26
|
4.9
|
20.2
|
1.0
|
O1B
|
A:ADP702
|
5.0
|
16.4
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 5jb2
Go back to
Fluorine Binding Sites List in 5jb2
Fluorine binding site 3 out
of 4 in the Crystal Structure of Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution.
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 Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F703
b:18.1
occ:1.00
|
F3
|
A:ALF703
|
0.0
|
18.1
|
1.0
|
AL
|
A:ALF703
|
1.8
|
18.5
|
1.0
|
F1
|
A:ALF703
|
2.5
|
19.1
|
1.0
|
F2
|
A:ALF703
|
2.6
|
17.2
|
1.0
|
O2B
|
A:ADP702
|
2.6
|
15.6
|
1.0
|
O
|
A:HOH852
|
2.7
|
17.0
|
1.0
|
NZ
|
A:LYS30
|
2.7
|
18.3
|
1.0
|
O
|
A:HOH817
|
2.7
|
17.5
|
1.0
|
CE
|
A:LYS30
|
3.3
|
18.0
|
1.0
|
CA
|
A:THR26
|
3.5
|
18.7
|
1.0
|
F4
|
A:ALF703
|
3.6
|
19.6
|
1.0
|
PB
|
A:ADP702
|
3.7
|
17.1
|
1.0
|
CB
|
A:ALA168
|
3.7
|
16.9
|
1.0
|
CG2
|
A:THR26
|
3.9
|
17.9
|
1.0
|
OE1
|
A:GLN465
|
4.0
|
19.6
|
1.0
|
CB
|
A:THR26
|
4.1
|
18.0
|
1.0
|
O1B
|
A:ADP702
|
4.1
|
16.4
|
1.0
|
N
|
A:GLY27
|
4.2
|
19.4
|
1.0
|
N
|
A:THR26
|
4.2
|
20.0
|
1.0
|
MG
|
A:MG704
|
4.2
|
17.7
|
1.0
|
O
|
A:HOH988
|
4.3
|
30.2
|
1.0
|
O
|
A:PRO25
|
4.3
|
18.6
|
1.0
|
O3B
|
A:ADP702
|
4.3
|
16.1
|
1.0
|
NE2
|
A:GLN465
|
4.3
|
20.0
|
1.0
|
N
|
A:ALA168
|
4.4
|
17.6
|
1.0
|
C
|
A:THR26
|
4.4
|
19.4
|
1.0
|
OE2
|
A:GLU132
|
4.5
|
17.0
|
1.0
|
C
|
A:PRO25
|
4.5
|
19.7
|
1.0
|
OE1
|
A:GLU132
|
4.6
|
17.7
|
1.0
|
CD
|
A:GLN465
|
4.6
|
19.4
|
1.0
|
CA
|
A:ALA168
|
4.7
|
17.4
|
1.0
|
NH2
|
A:ARG469
|
4.7
|
15.2
|
1.0
|
CD
|
A:LYS30
|
4.8
|
18.5
|
1.0
|
O
|
A:LEU24
|
4.8
|
18.9
|
1.0
|
CD
|
A:GLU132
|
5.0
|
17.2
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 5jb2
Go back to
Fluorine Binding Sites List in 5jb2
Fluorine binding site 4 out
of 4 in the Crystal Structure of Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution.
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 Chicken LGP2 with 5'Ppp 10-Mer Dsrna and Adp- ALF4-MG2+ at 2.2 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F703
b:19.6
occ:1.00
|
F4
|
A:ALF703
|
0.0
|
19.6
|
1.0
|
AL
|
A:ALF703
|
1.8
|
18.5
|
1.0
|
MG
|
A:MG704
|
2.3
|
17.7
|
1.0
|
F2
|
A:ALF703
|
2.5
|
17.2
|
1.0
|
F1
|
A:ALF703
|
2.6
|
19.1
|
1.0
|
O
|
A:HOH817
|
2.6
|
17.5
|
1.0
|
O2B
|
A:ADP702
|
2.7
|
15.6
|
1.0
|
O
|
A:HOH934
|
2.7
|
17.2
|
1.0
|
CA
|
A:GLY442
|
3.2
|
18.7
|
1.0
|
NH2
|
A:ARG471
|
3.2
|
20.8
|
1.0
|
O3B
|
A:ADP702
|
3.3
|
16.1
|
1.0
|
NH1
|
A:ARG469
|
3.4
|
15.9
|
1.0
|
O
|
A:GLY442
|
3.4
|
18.3
|
1.0
|
PB
|
A:ADP702
|
3.5
|
17.1
|
1.0
|
O
|
A:HOH819
|
3.5
|
15.7
|
1.0
|
F3
|
A:ALF703
|
3.6
|
18.1
|
1.0
|
N
|
A:GLY442
|
3.6
|
18.8
|
1.0
|
C
|
A:GLY442
|
3.6
|
18.3
|
1.0
|
OE2
|
A:GLU132
|
4.0
|
17.0
|
1.0
|
O2A
|
A:ADP702
|
4.1
|
17.3
|
1.0
|
CZ
|
A:ARG471
|
4.1
|
21.2
|
1.0
|
NH1
|
A:ARG471
|
4.1
|
21.8
|
1.0
|
O3A
|
A:ADP702
|
4.1
|
17.1
|
1.0
|
NH2
|
A:ARG469
|
4.3
|
15.2
|
1.0
|
CZ
|
A:ARG469
|
4.3
|
15.4
|
1.0
|
O
|
A:HOH828
|
4.6
|
16.9
|
1.0
|
PA
|
A:ADP702
|
4.7
|
17.3
|
1.0
|
N
|
A:LEU443
|
4.7
|
18.4
|
1.0
|
O1B
|
A:ADP702
|
4.9
|
16.4
|
1.0
|
C
|
A:GLU441
|
4.9
|
19.7
|
1.0
|
N
|
A:GLY27
|
4.9
|
19.4
|
1.0
|
O
|
A:LEU443
|
4.9
|
17.7
|
1.0
|
|
Reference:
E.Uchikawa,
M.Lethier,
H.Malet,
J.Brunel,
D.Gerlier,
S.Cusack.
Structural Analysis of Dsrna Binding to Anti-Viral Pattern Recognition Receptors LGP2 and MDA5. Mol.Cell V. 62 586 2016.
ISSN: ISSN 1097-2765
PubMed: 27203181
DOI: 10.1016/J.MOLCEL.2016.04.021
Page generated: Thu Aug 1 10:30:36 2024
|