Fluorine in PDB 4tz0: Dead-Box Helicase MSS116 Bound to Ssrna and Gdp-Bef

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

The structure of Dead-Box Helicase MSS116 Bound to Ssrna and Gdp-Bef, PDB code: 4tz0 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)	47.27 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.979, 126.614, 55.553, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 26

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

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Dead-Box Helicase MSS116 Bound to Ssrna and Gdp-Bef (pdb code 4tz0). 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 Gdp-Bef, PDB code: 4tz0:
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 Gdp-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 Gdp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:46.4 occ:1.00 F1 A:BEF602 0.0 46.4 1.0 BE A:BEF602 1.5 48.0 1.0 HZ3 A:LYS158 2.0 68.7 1.0 F3 A:BEF602 2.5 44.2 1.0 F2 A:BEF602 2.6 45.5 1.0 O A:HOH719 2.7 43.6 1.0 HG22 A:THR154 2.7 66.9 1.0 HA A:THR154 2.8 60.6 1.0 NZ A:LYS158 2.9 57.2 1.0 HB2 A:ALA306 3.0 61.7 1.0 O3B A:GDP601 3.1 49.0 1.0 O A:HOH732 3.2 45.4 1.0 HE2 A:LYS158 3.3 59.7 1.0 HE3 A:LYS158 3.3 59.7 1.0 HZ2 A:LYS158 3.3 68.7 1.0 HZ1 A:LYS158 3.4 68.7 1.0 CE A:LYS158 3.4 49.8 1.0 CG2 A:THR154 3.6 55.8 1.0 CA A:THR154 3.7 50.5 1.0 HB3 A:ALA306 3.7 61.7 1.0 CB A:ALA306 3.8 51.4 1.0 O A:HOH715 3.8 48.5 1.0 H A:GLY155 3.9 72.0 1.0 HH22 A:ARG466 3.9 55.9 1.0 O2B A:GDP601 3.9 52.0 1.0 PB A:GDP601 3.9 53.4 1.0 HB A:THR154 4.0 64.3 1.0 CB A:THR154 4.0 53.6 1.0 HG23 A:THR154 4.0 66.9 1.0 HH12 A:ARG469 4.1 43.0 1.0 H A:ALA306 4.1 66.2 1.0 MG A:MG603 4.2 46.3 1.0 OE2 A:GLU268 4.2 50.2 1.0 O1B A:GDP601 4.2 47.2 1.0 HG21 A:THR154 4.3 66.9 1.0 HH12 A:ARG466 4.4 57.8 1.0 HB1 A:ALA306 4.4 61.7 1.0 N A:THR154 4.4 52.5 1.0 HH22 A:ARG469 4.5 57.9 1.0 HE1 A:HIS462 4.5 63.2 1.0 N A:GLY155 4.5 60.0 1.0 N A:ALA306 4.5 55.2 1.0 H A:GLY439 4.5 54.0 1.0 HA2 A:GLY439 4.6 50.1 1.0 O A:LYS153 4.6 57.7 1.0 ND1 A:HIS462 4.7 52.4 1.0 C A:THR154 4.7 52.9 1.0 NH2 A:ARG466 4.7 46.6 1.0 CA A:ALA306 4.7 62.3 1.0 C A:LYS153 4.8 59.6 1.0 OE1 A:GLU268 4.9 46.8 1.0 H A:THR154 4.9 63.0 1.0 CD A:LYS158 4.9 44.8 1.0 O A:ALA152 4.9 57.1 1.0 NH1 A:ARG469 4.9 35.8 1.0 CE1 A:HIS462 4.9 52.6 1.0 CD A:GLU268 5.0 49.2 1.0 HA A:SER305 5.0 61.8 1.0

Fluorine binding site 2 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssrna and Gdp-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 Gdp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:45.5 occ:1.00 F2 A:BEF602 0.0 45.5 1.0 BE A:BEF602 1.6 48.0 1.0 MG A:MG603 2.0 46.3 1.0 F3 A:BEF602 2.5 44.2 1.0 HA2 A:GLY439 2.5 50.1 1.0 F1 A:BEF602 2.6 46.4 1.0 O3B A:GDP601 2.7 49.0 1.0 O A:HOH709 2.8 41.8 1.0 O1B A:GDP601 2.8 47.2 1.0 O A:HOH733 2.8 44.5 1.0 O A:HOH715 2.9 48.5 1.0 PB A:GDP601 3.3 53.4 1.0 OE2 A:GLU268 3.3 50.2 1.0 HH22 A:ARG469 3.4 57.9 1.0 HH22 A:ARG466 3.5 55.9 1.0 O A:HOH732 3.5 45.4 1.0 CA A:GLY439 3.5 41.7 1.0 HE2 A:LYS158 3.5 59.7 1.0 O A:HOH719 3.7 43.6 1.0 H A:GLY439 3.7 54.0 1.0 HZ3 A:LYS158 3.8 68.7 1.0 HA3 A:GLY439 3.9 50.1 1.0 O2B A:GDP601 4.0 52.0 1.0 N A:GLY439 4.0 45.0 1.0 O A:HOH716 4.1 46.1 1.0 NH2 A:ARG466 4.2 46.6 1.0 O A:GLY439 4.2 42.5 1.0 CE A:LYS158 4.2 49.8 1.0 NH2 A:ARG469 4.3 48.2 1.0 HH12 A:ARG469 4.3 43.0 1.0 HH21 A:ARG466 4.3 55.9 1.0 C A:GLY439 4.3 43.5 1.0 NZ A:LYS158 4.3 57.2 1.0 O2A A:GDP601 4.4 51.4 1.0 HE3 A:LYS158 4.4 59.7 1.0 CD A:GLU268 4.4 49.2 1.0 HZ2 A:LYS158 4.5 68.7 1.0 HB2 A:LYS158 4.5 56.0 1.0 O3A A:GDP601 4.6 58.4 1.0 H A:GLY155 4.6 72.0 1.0 HH21 A:ARG469 4.7 57.9 1.0 HA A:THR154 4.7 60.6 1.0 HG22 A:THR154 4.9 66.9 1.0 NH1 A:ARG469 5.0 35.8 1.0 OE1 A:GLU268 5.0 46.8 1.0

Fluorine binding site 3 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssrna and Gdp-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 Gdp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:44.2 occ:1.00 F3 A:BEF602 0.0 44.2 1.0 BE A:BEF602 1.5 48.0 1.0 HH22 A:ARG466 1.8 55.9 1.0 HH12 A:ARG469 1.9 43.0 1.0 O3B A:GDP601 2.3 49.0 1.0 HH22 A:ARG469 2.3 57.9 1.0 F2 A:BEF602 2.5 45.5 1.0 F1 A:BEF602 2.5 46.4 1.0 NH2 A:ARG466 2.6 46.6 1.0 NH1 A:ARG469 2.7 35.8 1.0 HH21 A:ARG466 2.9 55.9 1.0 NH2 A:ARG469 3.0 48.2 1.0 HB A:THR154 3.2 64.3 1.0 CZ A:ARG469 3.2 44.0 1.0 HH11 A:ARG469 3.3 43.0 1.0 H A:GLY155 3.3 72.0 1.0 HA A:THR154 3.3 60.6 1.0 HH12 A:ARG466 3.4 57.8 1.0 HG22 A:THR154 3.4 66.9 1.0 HA2 A:GLY439 3.5 50.1 1.0 O A:HOH732 3.6 45.4 1.0 CZ A:ARG466 3.6 43.0 1.0 H A:GLY439 3.6 54.0 1.0 PB A:GDP601 3.8 53.4 1.0 HH21 A:ARG469 3.8 57.9 1.0 NH1 A:ARG466 3.8 48.2 1.0 CB A:THR154 3.8 53.6 1.0 N A:GLY155 3.9 60.0 1.0 CA A:THR154 4.0 50.5 1.0 HZ3 A:LYS158 4.0 68.7 1.0 CG2 A:THR154 4.1 55.8 1.0 CA A:GLY439 4.2 41.7 1.0 O1B A:GDP601 4.2 47.2 1.0 O A:HOH709 4.3 41.8 1.0 N A:GLY439 4.3 45.0 1.0 MG A:MG603 4.3 46.3 1.0 C A:THR154 4.4 52.9 1.0 HG21 A:THR154 4.4 66.9 1.0 O2B A:GDP601 4.5 52.0 1.0 HA2 A:GLY155 4.5 67.4 1.0 O A:GLY439 4.5 42.5 1.0 O2A A:GDP601 4.5 51.4 1.0 NE A:ARG469 4.6 44.2 1.0 C A:GLY439 4.6 43.5 1.0 HH11 A:ARG466 4.7 57.8 1.0 O A:GLY465 4.7 52.1 1.0 NZ A:LYS158 4.8 57.2 1.0 CA A:GLY155 4.8 56.2 1.0 O3A A:GDP601 4.8 58.4 1.0 NE A:ARG466 4.8 49.4 1.0 O A:HOH719 4.8 43.6 1.0 HZ2 A:LYS158 4.8 68.7 1.0 HG23 A:THR154 4.9 66.9 1.0 OE2 A:GLU268 4.9 50.2 1.0 HE A:ARG466 4.9 59.3 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