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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

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