Atomistry » Fluorine » PDB 5j8m-5jw1 » 5jaj
Atomistry »
  Fluorine »
    PDB 5j8m-5jw1 »
      5jaj »

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

Go back to Fluorine Binding Sites List in 5jaj
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

Go back to Fluorine Binding Sites List in 5jaj
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

Go back to Fluorine Binding Sites List in 5jaj
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

Go back to Fluorine Binding Sites List in 5jaj
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

Go back to Fluorine Binding Sites List in 5jaj
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: Sun Dec 13 12:25:16 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy