Atomistry » Fluorine » PDB 5j8m-5jw1 » 5jb2
Atomistry »
  Fluorine »
    PDB 5j8m-5jw1 »
      5jb2 »

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:

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

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

Last articles

Na in 4GMM
Na in 4GM4
Na in 4GM1
Na in 4GM0
Na in 4GLY
Na in 4GIQ
Na in 4GIR
Na in 4GG1
Na in 4GK9
Na in 4GCV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy