Fluorine in PDB 4tyw: Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef

All present enzymatic activity of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef:
3.6.4.13;

The structure of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef, PDB code: 4tyw was solved by A.L.Mallam, D.J.Sidote, A.M.Lambowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.24 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.829, 126.260, 55.545, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.4

The structure of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef (pdb code 4tyw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef, PDB code: 4tyw:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:39.1 occ:1.00 F1 A:BEF603 0.0 39.1 1.0 BE A:BEF603 1.4 42.0 1.0 MG A:MG601 2.1 38.2 1.0 F2 A:BEF603 2.2 42.0 1.0 F3 A:BEF603 2.3 39.9 1.0 HA2 A:GLY439 2.5 39.6 1.0 O A:HOH800 2.8 40.5 1.0 O1B A:ADP604 2.9 45.3 1.0 O A:HOH801 2.9 35.6 1.0 O A:HOH799 3.0 35.2 1.0 O2B A:ADP604 3.0 35.2 1.0 OE2 A:GLU268 3.1 39.1 1.0 O A:HOH710 3.2 35.7 1.0 PB A:ADP604 3.3 40.9 1.0 CA A:GLY439 3.4 33.0 1.0 H A:GLY439 3.5 42.0 1.0 HH22 A:ARG469 3.5 45.8 1.0 HE2 A:LYS158 3.6 49.6 1.0 HZ3 A:LYS158 3.6 51.0 1.0 O A:HOH711 3.7 34.6 1.0 HH12 A:ARG466 3.7 47.1 1.0 HH22 A:ARG466 3.8 47.6 1.0 N A:GLY439 3.9 35.0 1.0 HA3 A:GLY439 3.9 39.6 1.0 O3B A:ADP604 4.1 38.8 1.0 O A:GLY439 4.2 35.5 1.0 O A:HOH802 4.2 36.1 1.0 HH12 A:ARG469 4.2 43.7 1.0 CE A:LYS158 4.3 41.4 1.0 C A:GLY439 4.3 35.3 1.0 NZ A:LYS158 4.3 42.5 1.0 HG22 A:THR154 4.3 57.9 1.0 NH2 A:ARG469 4.3 38.2 1.0 CD A:GLU268 4.3 39.3 1.0 HE3 A:LYS158 4.4 49.6 1.0 H A:GLY155 4.4 55.2 1.0 HZ2 A:LYS158 4.4 51.0 1.0 HA A:THR154 4.5 51.3 1.0 NH1 A:ARG466 4.5 39.3 1.0 O2A A:ADP604 4.5 38.5 1.0 NH2 A:ARG466 4.6 39.6 1.0 HB2 A:LYS158 4.7 46.5 1.0 O3A A:ADP604 4.7 42.8 1.0 HH21 A:ARG469 4.8 45.8 1.0 NH1 A:ARG469 4.9 36.4 1.0 OE1 A:GLU268 5.0 38.8 1.0

Fluorine binding site 2 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:42.0 occ:1.00 F2 A:BEF603 0.0 42.0 1.0 BE A:BEF603 1.4 42.0 1.0 HZ3 A:LYS158 2.0 51.0 1.0 F1 A:BEF603 2.2 39.1 1.0 F3 A:BEF603 2.3 39.9 1.0 HG22 A:THR154 2.5 57.9 1.0 O A:HOH711 2.6 34.6 1.0 HA A:THR154 2.7 51.3 1.0 NZ A:LYS158 2.9 42.5 1.0 HB2 A:ALA306 3.1 55.3 1.0 O A:HOH710 3.1 35.7 1.0 O1B A:ADP604 3.2 45.3 1.0 HE2 A:LYS158 3.2 49.6 1.0 HE3 A:LYS158 3.3 49.6 1.0 HZ2 A:LYS158 3.3 51.0 1.0 CE A:LYS158 3.4 41.4 1.0 CG2 A:THR154 3.4 48.2 1.0 HZ1 A:LYS158 3.4 51.0 1.0 HH22 A:ARG466 3.4 47.6 1.0 CA A:THR154 3.6 42.7 1.0 HG23 A:THR154 3.8 57.9 1.0 O A:HOH800 3.8 40.5 1.0 H A:GLY155 3.8 55.2 1.0 PB A:ADP604 3.8 40.9 1.0 CB A:THR154 3.9 44.6 1.0 HB A:THR154 3.9 53.5 1.0 O3B A:ADP604 3.9 38.8 1.0 CB A:ALA306 3.9 46.1 1.0 HB3 A:ALA306 3.9 55.3 1.0 OE2 A:GLU268 4.0 39.1 1.0 MG A:MG601 4.0 38.2 1.0 HG21 A:THR154 4.0 57.9 1.0 H A:ALA306 4.1 53.3 1.0 HH12 A:ARG469 4.1 43.7 1.0 O2B A:ADP604 4.2 35.2 1.0 NH2 A:ARG466 4.3 39.6 1.0 HA2 A:GLY439 4.4 39.6 1.0 N A:THR154 4.4 44.2 1.0 H A:GLY439 4.4 42.0 1.0 HH22 A:ARG469 4.4 45.8 1.0 N A:GLY155 4.5 46.0 1.0 HH12 A:ARG466 4.5 47.1 1.0 HB1 A:ALA306 4.5 55.3 1.0 N A:ALA306 4.5 44.5 1.0 HE1 A:HIS462 4.6 52.5 1.0 HH21 A:ARG466 4.6 47.6 1.0 C A:THR154 4.6 45.5 1.0 ND1 A:HIS462 4.7 40.0 1.0 O A:LYS153 4.7 46.2 1.0 H A:THR154 4.8 53.0 1.0 CA A:ALA306 4.8 47.6 1.0 C A:LYS153 4.8 45.9 1.0 CD A:GLU268 4.9 39.3 1.0 O A:HOH801 4.9 35.6 1.0 CD A:LYS158 4.9 41.8 1.0 O A:ALA152 4.9 50.7 1.0 OE1 A:GLU268 4.9 38.8 1.0 HA A:SER305 5.0 52.2 1.0 NH1 A:ARG469 5.0 36.4 1.0 HB2 A:LYS158 5.0 46.5 1.0

Fluorine binding site 3 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dead-Box Helicase MSS116 Bound to Ssrna and Adp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:39.9 occ:1.00 F3 A:BEF603 0.0 39.9 1.0 BE A:BEF603 1.4 42.0 1.0 HH22 A:ARG466 2.1 47.6 1.0 HH12 A:ARG469 2.2 43.7 1.0 F1 A:BEF603 2.3 39.1 1.0 F2 A:BEF603 2.3 42.0 1.0 HH12 A:ARG466 2.4 47.1 1.0 O1B A:ADP604 2.7 45.3 1.0 HH22 A:ARG469 2.7 45.8 1.0 NH2 A:ARG466 2.8 39.6 1.0 HG22 A:THR154 2.9 57.9 1.0 NH1 A:ARG469 3.0 36.4 1.0 O A:HOH710 3.0 35.7 1.0 NH1 A:ARG466 3.1 39.3 1.0 HB A:THR154 3.1 53.5 1.0 H A:GLY155 3.3 55.2 1.0 HA A:THR154 3.3 51.3 1.0 H A:GLY439 3.3 42.0 1.0 HA2 A:GLY439 3.4 39.6 1.0 CZ A:ARG466 3.4 36.0 1.0 NH2 A:ARG469 3.4 38.2 1.0 HH21 A:ARG466 3.5 47.6 1.0 CG2 A:THR154 3.6 48.2 1.0 HH11 A:ARG469 3.6 43.7 1.0 CZ A:ARG469 3.6 37.7 1.0 CB A:THR154 3.7 44.6 1.0 HH11 A:ARG466 3.9 47.1 1.0 HZ3 A:LYS158 3.9 51.0 1.0 HG21 A:THR154 3.9 57.9 1.0 CA A:THR154 3.9 42.7 1.0 PB A:ADP604 3.9 40.9 1.0 N A:GLY155 4.0 46.0 1.0 N A:GLY439 4.0 35.0 1.0 CA A:GLY439 4.0 33.0 1.0 HH21 A:ARG469 4.2 45.8 1.0 MG A:MG601 4.2 38.2 1.0 O A:HOH799 4.4 35.2 1.0 O2B A:ADP604 4.4 35.2 1.0 HG23 A:THR154 4.4 57.9 1.0 C A:THR154 4.4 45.5 1.0 O A:GLY439 4.5 35.5 1.0 C A:GLY439 4.5 35.3 1.0 O A:HOH711 4.6 34.6 1.0 OE2 A:GLU268 4.6 39.1 1.0 O3B A:ADP604 4.7 38.8 1.0 NE A:ARG466 4.7 35.9 1.0 NZ A:LYS158 4.7 42.5 1.0 HA2 A:GLY155 4.8 50.3 1.0 HZ2 A:LYS158 4.9 51.0 1.0 O A:GLY465 4.9 42.7 1.0 HA3 A:GLY439 4.9 39.6 1.0 O2A A:ADP604 4.9 38.5 1.0 O A:HOH801 4.9 35.6 1.0 NE A:ARG469 4.9 38.1 1.0 HB2 A:ALA306 5.0 55.3 1.0 O A:HOH800 5.0 40.5 1.0 CA A:GLY155 5.0 41.9 1.0 HE2 A:LYS158 5.0 49.6 1.0

A.L.Mallam, D.J.Sidote, A.M.Lambowitz. Molecular Insights Into Rna and Dna Helicase Evolution From the Determinants of Specificity For A Dead-Box Rna Helicase. Elife V. 4 2014.
ISSN: ESSN 2050-084X
PubMed: 25497230
DOI: 10.7554/ELIFE.04630