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Fluorine in PDB 5jaj: Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.

Protein crystallography data

The structure of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg., PDB code: 5jaj 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) 76.08 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.590, 97.050, 122.520, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 16.8

Other elements in 5jaj:

The structure of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 1 atom
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. (pdb code 5jaj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg., PDB code: 5jaj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 5jaj

Go back to Fluorine Binding Sites List in 5jaj
Fluorine binding site 1 out of 7 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F703

b:20.8
occ:1.00
 F1 A:ALF703 0.0 20.8 1.0
AL A:ALF703 1.8 17.6 1.0
MG A:MG704 2.0 18.9 1.0
F4 A:ALF703 2.5 25.2 1.0
F3 A:ALF703 2.5 18.0 1.0
O A:HOH836 2.6 16.1 1.0
O3B A:ADP702 2.7 19.2 1.0
O2B A:ADP702 2.8 18.1 1.0
O A:HOH851 2.9 17.8 1.0
O A:HOH1059 3.0 26.5 1.0
OE2 A:GLU132 3.2 17.8 1.0
PB A:ADP702 3.2 18.5 1.0
O A:HOH922 3.5 20.9 1.0
O A:HOH872 3.5 16.4 1.0
CE A:LYS30 3.5 18.8 1.0
F2 A:ALF703 3.6 20.2 1.0
NZ A:LYS30 3.7 18.2 1.0
O A:HOH990 3.8 18.4 1.0
CD A:GLU132 3.9 16.8 1.0
O1B A:ADP702 4.0 19.0 1.0
OE1 A:GLU132 4.2 17.8 1.0
O3A A:ADP702 4.6 18.7 1.0
CA A:GLY442 4.6 17.8 1.0
OD1 A:ASP131 4.6 20.5 1.0
N A:GLY442 4.8 16.5 1.0
CD A:LYS30 4.9 18.2 1.0

Fluorine binding site 2 out of 7 in 5jaj

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Fluorine binding site 2 out of 7 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F703

b:20.2
occ:1.00
 F2 A:ALF703 0.0 20.2 1.0
AL A:ALF703 1.8 17.6 1.0
F4 A:ALF703 2.5 25.2 1.0
O2B A:ADP702 2.5 18.1 1.0
F3 A:ALF703 2.5 18.0 1.0
O A:HOH836 2.6 16.1 1.0
NH2 A:ARG469 2.8 17.5 1.0
NH1 A:ARG471 2.8 18.9 1.0
NH1 A:ARG469 3.2 17.2 1.0
CB A:THR26 3.3 19.5 1.0
N A:GLY27 3.3 17.8 1.0
CA A:THR26 3.4 18.3 1.0
CZ A:ARG469 3.4 16.4 1.0
NH2 A:ARG471 3.4 20.4 1.0
CZ A:ARG471 3.6 19.2 1.0
F1 A:ALF703 3.6 20.8 1.0
CG2 A:THR26 3.6 18.3 1.0
C A:THR26 3.8 17.9 1.0
PB A:ADP702 4.1 18.5 1.0
OE1 A:GLN465 4.1 16.6 1.0
CA A:GLY27 4.4 18.5 1.0
OG1 A:THR26 4.6 21.0 1.0
MG A:MG704 4.7 18.9 1.0
N A:GLY442 4.7 16.5 1.0
N A:THR26 4.7 18.3 1.0
O3A A:ADP702 4.7 18.7 1.0
NE A:ARG469 4.7 17.1 1.0
O3B A:ADP702 4.7 19.2 1.0
NZ A:LYS30 4.8 18.2 1.0
O A:GLY468 4.8 18.1 1.0
NE A:ARG471 4.9 21.6 1.0
O A:HOH872 4.9 16.4 1.0
O A:THR26 4.9 20.0 1.0
O1B A:ADP702 5.0 19.0 1.0

Fluorine binding site 3 out of 7 in 5jaj

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Fluorine binding site 3 out of 7 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F703

b:18.0
occ:1.00
 F3 A:ALF703 0.0 18.0 1.0
AL A:ALF703 1.8 17.6 1.0
F1 A:ALF703 2.5 20.8 1.0
F2 A:ALF703 2.5 20.2 1.0
O A:HOH836 2.6 16.1 1.0
O2B A:ADP702 2.6 18.1 1.0
NZ A:LYS30 2.7 18.2 1.0
O A:HOH872 2.7 16.4 1.0
CE A:LYS30 3.4 18.8 1.0
CA A:THR26 3.4 18.3 1.0
F4 A:ALF703 3.5 25.2 1.0
CB A:ALA168 3.7 17.8 1.0
CG2 A:THR26 3.7 18.3 1.0
PB A:ADP702 3.8 18.5 1.0
CB A:THR26 3.9 19.5 1.0
OE1 A:GLN465 4.0 16.6 1.0
N A:THR26 4.1 18.3 1.0
N A:GLY27 4.1 17.8 1.0
O1B A:ADP702 4.1 19.0 1.0
O A:PRO25 4.2 18.7 1.0
O3B A:ADP702 4.3 19.2 1.0
C A:THR26 4.3 17.9 1.0
MG A:MG704 4.3 18.9 1.0
NE2 A:GLN465 4.3 17.7 1.0
N A:ALA168 4.3 15.6 1.0
C A:PRO25 4.5 18.7 1.0
OE2 A:GLU132 4.5 17.8 1.0
O A:HOH1059 4.5 26.5 1.0
CD A:GLN465 4.6 15.6 1.0
CA A:ALA168 4.6 16.2 1.0
NH2 A:ARG469 4.7 17.5 1.0
OE1 A:GLU132 4.7 17.8 1.0
O A:LEU24 4.8 18.0 1.0
CD A:LYS30 4.8 18.2 1.0

Fluorine binding site 4 out of 7 in 5jaj

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Fluorine binding site 4 out of 7 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F703

b:25.2
occ:1.00
 F4 A:ALF703 0.0 25.2 1.0
AL A:ALF703 1.8 17.6 1.0
F2 A:ALF703 2.5 20.2 1.0
F1 A:ALF703 2.5 20.8 1.0
MG A:MG704 2.6 18.9 1.0
O2B A:ADP702 2.6 18.1 1.0
O A:HOH836 2.6 16.1 1.0
O A:HOH990 2.9 18.4 1.0
NH2 A:ARG471 3.1 20.4 1.0
CA A:GLY442 3.2 17.8 1.0
O3B A:ADP702 3.3 19.2 1.0
NH1 A:ARG469 3.3 17.2 1.0
O A:HOH851 3.4 17.8 1.0
PB A:ADP702 3.4 18.5 1.0
O A:GLY442 3.5 18.3 1.0
F3 A:ALF703 3.5 18.0 1.0
N A:GLY442 3.6 16.5 1.0
C A:GLY442 3.6 16.6 1.0
CZ A:ARG471 4.0 19.2 1.0
OE2 A:GLU132 4.0 17.8 1.0
NH1 A:ARG471 4.0 18.9 1.0
O2A A:ADP702 4.0 22.0 1.0
O3A A:ADP702 4.1 18.7 1.0
NH2 A:ARG469 4.2 17.5 1.0
CZ A:ARG469 4.2 16.4 1.0
O A:HOH922 4.6 20.9 1.0
PA A:ADP702 4.7 19.5 1.0
N A:LEU443 4.7 16.7 1.0
N A:GLY27 4.8 17.8 1.0
O1B A:ADP702 4.8 19.0 1.0
C A:GLU441 4.9 15.8 1.0
O A:LEU443 4.9 17.4 1.0

Fluorine binding site 5 out of 7 in 5jaj

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Fluorine binding site 5 out of 7 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F101

b:35.7
occ:1.00
 F1 Y:MGF101 0.0 35.7 1.0
MG Y:MGF101 1.9 29.7 1.0
N2 Y:G6 2.7 17.8 1.0
F2 Y:MGF101 3.0 25.4 1.0
O X:HOH126 3.0 29.7 1.0
F3 Y:MGF101 3.3 48.9 1.0
C2 Y:G6 3.7 16.3 1.0
O Y:HOH208 3.8 30.6 1.0
O X:HOH107 3.8 45.7 1.0
N3 Y:G6 3.8 14.1 1.0
C1' X:G6 3.9 18.1 1.0
C1' Y:U7 3.9 14.8 1.0
O2 Y:U7 4.0 18.0 1.0
N3 X:G6 4.1 17.4 1.0
O2 X:C5 4.2 22.3 1.0
O2' Y:U7 4.4 15.9 1.0
C4 X:G6 4.4 16.6 1.0
O4' Y:U7 4.4 15.2 1.0
N9 X:G6 4.4 16.6 1.0
O A:HOH1235 4.4 39.6 1.0
O4' X:G6 4.4 19.2 1.0
C2 Y:U7 4.5 14.9 1.0
NZ A:LYS56 4.5 27.8 0.5
N1 Y:U7 4.6 14.3 1.0
O2' X:G6 4.6 20.8 1.0
O A:HOH879 4.7 41.9 1.0
O A:HOH1184 4.7 31.5 1.0
C2' Y:U7 4.8 14.1 1.0
C2' X:G6 4.8 18.9 1.0
C2 X:G6 4.8 16.6 1.0
N1 Y:G6 4.9 17.5 1.0

Fluorine binding site 6 out of 7 in 5jaj

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Fluorine binding site 6 out of 7 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F101

b:25.4
occ:1.00
 F2 Y:MGF101 0.0 25.4 1.0
MG Y:MGF101 1.7 29.7 1.0
N3 Y:G6 2.6 14.1 1.0
O2' Y:G6 2.8 16.1 1.0
F3 Y:MGF101 2.8 48.9 1.0
O X:HOH126 2.8 29.7 1.0
F1 Y:MGF101 3.0 35.7 1.0
C2' Y:G6 3.1 13.8 1.0
C1' Y:G6 3.2 14.4 1.0
O4' Y:U7 3.4 15.2 1.0
O X:HOH136 3.5 32.6 1.0
C2 Y:G6 3.5 16.3 1.0
C4 Y:G6 3.6 15.4 1.0
N2 X:G6 3.6 16.6 1.0
N2 Y:G6 3.6 17.8 1.0
N9 Y:G6 3.8 13.8 1.0
C1' Y:U7 3.9 14.8 1.0
N3 X:G6 3.9 17.4 1.0
O A:HOH987 3.9 23.8 1.0
C2 X:G6 4.0 16.6 1.0
N1 Y:U7 4.3 14.3 1.0
O4' Y:G6 4.4 14.5 1.0
OG A:SER437 4.6 20.5 1.0
C4' Y:U7 4.6 14.3 1.0
C3' Y:G6 4.6 13.3 1.0
O A:HOH1220 4.6 27.4 1.0
C6 Y:U7 4.7 14.6 1.0
N1 Y:G6 4.8 17.5 1.0
C2 Y:U7 4.9 14.9 1.0
C5 Y:G6 4.9 14.9 1.0
C4 X:G6 4.9 16.6 1.0
N1 X:G6 5.0 16.9 1.0

Fluorine binding site 7 out of 7 in 5jaj

Go back to Fluorine Binding Sites List in 5jaj
Fluorine binding site 7 out of 7 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F101

b:48.9
occ:1.00
 F3 Y:MGF101 0.0 48.9 1.0
MG Y:MGF101 1.9 29.7 1.0
O A:HOH1235 2.5 39.6 1.0
O A:HOH987 2.5 23.8 1.0
F2 Y:MGF101 2.8 25.4 1.0
NZ A:LYS56 3.0 27.8 0.5
O X:HOH126 3.0 29.7 1.0
F1 Y:MGF101 3.3 35.7 1.0
O A:HOH919 3.6 37.0 1.0
O X:HOH125 4.0 39.9 1.0
NZ A:LYS56 4.0 19.3 0.5
O4' Y:U7 4.1 15.2 1.0
O2' Y:G6 4.1 16.1 1.0
CE A:LYS56 4.1 19.7 0.5
CE A:LYS56 4.2 27.7 0.5
OG A:SER437 4.2 20.5 1.0
O X:HOH136 4.4 32.6 1.0
O A:HOH1184 4.5 31.5 1.0
O2' Y:U7 4.6 15.9 1.0
C4' Y:U7 4.6 14.3 1.0
C1' Y:U7 4.6 14.8 1.0
OE2 A:GLU440 4.9 26.6 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 10:30:37 2024

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