Fluorine in PDB 5e3h: Structural Basis For Rna Recognition and Activation of Rig-I

All present enzymatic activity of Structural Basis For Rna Recognition and Activation of Rig-I:
3.6.4.13;

The structure of Structural Basis For Rna Recognition and Activation of Rig-I, PDB code: 5e3h was solved by F.Jiang, M.T.Miller, J.Marcotrigiano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.97 / 2.70
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	176.030, 176.030, 108.071, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 26.8

The structure of Structural Basis For Rna Recognition and Activation of Rig-I also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the Structural Basis For Rna Recognition and Activation of Rig-I (pdb code 5e3h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structural Basis For Rna Recognition and Activation of Rig-I, PDB code: 5e3h:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structural Basis For Rna Recognition and Activation of Rig-I


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Basis For Rna Recognition and Activation of Rig-I within 5.0Å range: probe atom residue distance (Å) B Occ A:F1007 b:76.8 occ:1.00 F1 A:BEF1007 0.0 76.8 1.0 BE A:BEF1007 1.5 72.8 1.0 MG A:MG1003 2.5 78.1 1.0 F3 A:BEF1007 2.5 65.8 1.0 F2 A:BEF1007 2.6 65.8 1.0 O3B A:ADP1006 2.7 0.8 1.0 O1B A:ADP1006 3.1 86.3 1.0 NZ A:LYS270 3.2 76.7 1.0 OE2 A:GLU373 3.2 55.8 1.0 PB A:ADP1006 3.4 98.5 1.0 O2B A:ADP1006 3.8 85.0 1.0 CD A:GLU373 4.3 66.4 1.0 O A:GLU702 4.5 0.1 1.0 CG2 A:THR266 4.6 46.7 1.0 CE A:LYS270 4.6 74.5 1.0 OE1 A:GLU373 4.8 70.4 1.0 O1A A:ADP1006 4.8 70.7 1.0 O3A A:ADP1006 4.9 80.0 1.0 OD2 A:ASP372 5.0 72.5 1.0

Fluorine binding site 2 out of 3 in the Structural Basis For Rna Recognition and Activation of Rig-I


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Basis For Rna Recognition and Activation of Rig-I within 5.0Å range: probe atom residue distance (Å) B Occ A:F1007 b:65.8 occ:1.00 F2 A:BEF1007 0.0 65.8 1.0 BE A:BEF1007 1.6 72.8 1.0 F3 A:BEF1007 2.5 65.8 1.0 F1 A:BEF1007 2.6 76.8 1.0 OG1 A:THR266 2.9 46.6 1.0 NZ A:LYS270 3.2 76.7 1.0 CB A:THR266 3.6 46.5 1.0 CG2 A:THR266 3.7 46.7 1.0 CA A:THR266 3.8 46.5 1.0 CB A:ALA410 3.9 46.0 1.0 OE2 A:GLU373 3.9 55.8 1.0 O1B A:ADP1006 4.2 86.3 1.0 CE A:LYS270 4.2 74.5 1.0 N A:ALA410 4.3 46.5 1.0 O2B A:ADP1006 4.3 85.0 1.0 OE1 A:GLU373 4.4 70.4 1.0 N A:THR266 4.4 46.5 1.0 O3B A:ADP1006 4.6 0.8 1.0 CD A:GLU373 4.6 66.4 1.0 PB A:ADP1006 4.6 98.5 1.0 CA A:ALA410 4.7 46.3 1.0 CG A:GLN726 4.8 64.1 1.0 O A:GLU702 4.8 0.1 1.0 C A:THR409 4.9 50.2 1.0 MG A:MG1003 5.0 78.1 1.0

Fluorine binding site 3 out of 3 in the Structural Basis For Rna Recognition and Activation of Rig-I


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural Basis For Rna Recognition and Activation of Rig-I within 5.0Å range: probe atom residue distance (Å) B Occ A:F1007 b:65.8 occ:1.00 F3 A:BEF1007 0.0 65.8 1.0 BE A:BEF1007 1.5 72.8 1.0 O A:GLU702 2.4 0.1 1.0 F2 A:BEF1007 2.5 65.8 1.0 F1 A:BEF1007 2.5 76.8 1.0 OE2 A:GLU373 3.1 55.8 1.0 C A:GLU702 3.4 0.9 1.0 CG2 A:THR266 3.9 46.7 1.0 CD A:GLU373 4.0 66.4 1.0 OG1 A:THR266 4.1 46.6 1.0 CA A:GLU702 4.2 0.4 1.0 N A:GLY703 4.3 0.8 1.0 OE1 A:GLU373 4.3 70.4 1.0 CA A:GLY703 4.4 0.4 1.0 O1B A:ADP1006 4.5 86.3 1.0 CB A:THR266 4.7 46.5 1.0 MG A:MG1003 4.7 78.1 1.0 CG A:GLN726 4.9 64.1 1.0 NE2 A:GLN726 4.9 75.2 1.0

F.Jiang, A.Ramanathan, M.T.Miller, G.Q.Tang, M.Gale, S.S.Patel, J.Marcotrigiano. Structural Basis of Rna Recognition and Activation By Innate Immune Receptor Rig-I. Nature V. 479 423 2011.
ISSN: ESSN 1476-4687
PubMed: 21947008
DOI: 10.1038/NATURE10537