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Fluorine in PDB 5jbg: Crystal Structure of Chicken LGP2 with 5'Ppp 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution.

Protein crystallography data

The structure of Crystal Structure of Chicken LGP2 with 5'Ppp 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution., PDB code: 5jbg 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) 76.27 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.860, 97.430, 122.580, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.5

Other elements in 5jbg:

The structure of Crystal Structure of Chicken LGP2 with 5'Ppp 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
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 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution. (pdb code 5jbg). 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 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution., PDB code: 5jbg:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5jbg

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Fluorine binding site 1 out of 4 in the Crystal Structure of Chicken LGP2 with 5'Ppp 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 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 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F703

b:26.6
occ:1.00
F1 A:ALF703 0.0 26.6 1.0
AL A:ALF703 1.8 24.8 1.0
MG A:MG704 2.0 25.6 1.0
F3 A:ALF703 2.5 26.0 1.0
O A:HOH805 2.6 19.4 1.0
F4 A:ALF703 2.6 27.3 1.0
O A:HOH958 2.6 28.7 1.0
O3B A:ADP702 2.7 25.9 1.0
O1B A:ADP702 2.8 24.5 1.0
O A:HOH814 3.1 21.6 1.0
PB A:ADP702 3.2 26.1 1.0
OE2 A:GLU132 3.2 26.9 1.0
CE A:LYS30 3.3 24.7 1.0
O A:HOH832 3.4 26.4 1.0
O A:HOH835 3.4 27.0 1.0
F2 A:ALF703 3.6 23.8 1.0
NZ A:LYS30 3.7 25.0 1.0
O A:HOH931 3.9 25.1 1.0
O2B A:ADP702 3.9 26.2 1.0
CD A:GLU132 4.0 26.9 1.0
OE1 A:GLU132 4.2 29.4 1.0
OD1 A:ASP131 4.6 29.2 1.0
O3A A:ADP702 4.6 28.0 1.0
CA A:GLY442 4.7 25.5 1.0
CD A:LYS30 4.7 25.1 1.0
N A:GLY442 4.9 25.6 1.0

Fluorine binding site 2 out of 4 in 5jbg

Go back to Fluorine Binding Sites List in 5jbg
Fluorine binding site 2 out of 4 in the Crystal Structure of Chicken LGP2 with 5'Ppp 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 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 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F703

b:23.8
occ:1.00
F2 A:ALF703 0.0 23.8 1.0
AL A:ALF703 1.8 24.8 1.0
F4 A:ALF703 2.5 27.3 1.0
F3 A:ALF703 2.6 26.0 1.0
O1B A:ADP702 2.6 24.5 1.0
NH1 A:ARG471 2.8 28.7 1.0
NH2 A:ARG469 2.8 23.4 1.0
O A:HOH805 2.8 19.4 1.0
NH1 A:ARG469 3.2 22.8 1.0
NH2 A:ARG471 3.2 30.8 1.0
CB A:THR26 3.3 24.2 1.0
N A:GLY27 3.3 23.7 1.0
CZ A:ARG469 3.4 23.1 1.0
CA A:THR26 3.4 24.4 1.0
CZ A:ARG471 3.5 29.6 1.0
F1 A:ALF703 3.6 26.6 1.0
CG2 A:THR26 3.7 24.1 1.0
C A:THR26 3.8 24.2 1.0
PB A:ADP702 4.0 26.1 1.0
OE1 A:GLN465 4.2 25.8 1.0
CA A:GLY27 4.3 25.2 1.0
MG A:MG704 4.5 25.6 1.0
OG1 A:THR26 4.6 25.5 1.0
N A:GLY442 4.6 25.6 1.0
O3B A:ADP702 4.7 25.9 1.0
O3A A:ADP702 4.7 28.0 1.0
NE A:ARG469 4.7 25.0 1.0
NE A:ARG471 4.8 30.9 1.0
N A:THR26 4.8 24.4 1.0
NZ A:LYS30 4.8 25.0 1.0
O A:GLY468 4.9 24.3 1.0
O A:THR26 4.9 23.1 1.0
CA A:GLY442 5.0 25.5 1.0

Fluorine binding site 3 out of 4 in 5jbg

Go back to Fluorine Binding Sites List in 5jbg
Fluorine binding site 3 out of 4 in the Crystal Structure of Chicken LGP2 with 5'Ppp 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 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 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F703

b:26.0
occ:1.00
F3 A:ALF703 0.0 26.0 1.0
AL A:ALF703 1.8 24.8 1.0
F1 A:ALF703 2.5 26.6 1.0
F2 A:ALF703 2.6 23.8 1.0
O1B A:ADP702 2.7 24.5 1.0
O A:HOH805 2.7 19.4 1.0
NZ A:LYS30 2.7 25.0 1.0
O A:HOH832 2.8 26.4 1.0
CE A:LYS30 3.3 24.7 1.0
CA A:THR26 3.4 24.4 1.0
F4 A:ALF703 3.6 27.3 1.0
CB A:ALA168 3.6 22.7 1.0
CG2 A:THR26 3.7 24.1 1.0
PB A:ADP702 3.8 26.1 1.0
CB A:THR26 3.9 24.2 1.0
OE1 A:GLN465 4.0 25.8 1.0
N A:GLY27 4.1 23.7 1.0
O2B A:ADP702 4.2 26.2 1.0
N A:THR26 4.2 24.4 1.0
O A:PRO25 4.2 23.2 1.0
O A:HOH958 4.3 28.7 1.0
MG A:MG704 4.3 25.6 1.0
C A:THR26 4.3 24.2 1.0
O3B A:ADP702 4.3 25.9 1.0
N A:ALA168 4.4 23.9 1.0
NE2 A:GLN465 4.4 26.0 1.0
C A:PRO25 4.5 25.1 1.0
OE2 A:GLU132 4.5 26.9 1.0
NH2 A:ARG469 4.6 23.4 1.0
CA A:ALA168 4.6 23.0 1.0
CD A:GLN465 4.7 25.7 1.0
OE1 A:GLU132 4.7 29.4 1.0
CD A:LYS30 4.8 25.1 1.0
O A:LEU24 4.8 26.9 1.0

Fluorine binding site 4 out of 4 in 5jbg

Go back to Fluorine Binding Sites List in 5jbg
Fluorine binding site 4 out of 4 in the Crystal Structure of Chicken LGP2 with 5'Ppp 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 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 26-Mer Hairpin Rna with 3' Gg Overhang and Adp-ALF4-MG2+ at 2.0 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F703

b:27.3
occ:1.00
F4 A:ALF703 0.0 27.3 1.0
AL A:ALF703 1.8 24.8 1.0
MG A:MG704 2.4 25.6 1.0
F2 A:ALF703 2.5 23.8 1.0
F1 A:ALF703 2.6 26.6 1.0
O A:HOH805 2.7 19.4 1.0
O1B A:ADP702 2.8 24.5 1.0
O A:HOH931 2.9 25.1 1.0
NH2 A:ARG471 3.1 30.8 1.0
CA A:GLY442 3.2 25.5 1.0
O3B A:ADP702 3.2 25.9 1.0
O A:GLY442 3.4 25.7 1.0
NH1 A:ARG469 3.4 22.8 1.0
PB A:ADP702 3.5 26.1 1.0
N A:GLY442 3.5 25.6 1.0
C A:GLY442 3.6 24.1 1.0
F3 A:ALF703 3.6 26.0 1.0
O A:HOH814 3.6 21.6 1.0
O1A A:ADP702 3.9 27.1 1.0
OE2 A:GLU132 4.0 26.9 1.0
CZ A:ARG471 4.1 29.6 1.0
O3A A:ADP702 4.1 28.0 1.0
NH1 A:ARG471 4.2 28.7 1.0
NH2 A:ARG469 4.2 23.4 1.0
CZ A:ARG469 4.3 23.1 1.0
O A:HOH835 4.4 27.0 1.0
PA A:ADP702 4.6 27.5 1.0
N A:LEU443 4.7 24.0 1.0
C A:GLU441 4.9 26.4 1.0
O2B A:ADP702 4.9 26.2 1.0
N A:GLY27 4.9 23.7 1.0
O A:LEU443 5.0 22.5 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 12:25:17 2020

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