Fluorine in PDB 4tyn: Dead-Box Helicase MSS116 Bound to Ssdna and Adp-Bef

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

The structure of Dead-Box Helicase MSS116 Bound to Ssdna and Adp-Bef, PDB code: 4tyn 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)	44.15 / 2.96
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.389, 126.189, 55.231, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.4

The structure of Dead-Box Helicase MSS116 Bound to Ssdna and Adp-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 Ssdna and Adp-Bef (pdb code 4tyn). 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 Ssdna and Adp-Bef, PDB code: 4tyn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssdna 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 Ssdna and Adp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:47.7 occ:1.00 F1 A:BEF602 0.0 47.7 1.0 BE A:BEF602 1.5 34.2 1.0 OE2 A:GLU268 2.2 49.6 1.0 F3 A:BEF602 2.5 36.1 1.0 HA2 A:GLY439 2.5 50.6 1.0 F2 A:BEF602 2.6 30.9 1.0 HA3 A:GLY439 2.7 50.6 1.0 CA A:GLY439 3.0 42.1 1.0 HG2 A:GLU268 3.2 48.6 1.0 CD A:GLU268 3.2 46.4 1.0 OD2 A:ASP267 3.3 43.1 1.0 HD21 A:LEU192 3.4 39.9 1.0 HD11 A:LEU192 3.4 32.0 1.0 OD1 A:ASP267 3.5 39.8 1.0 CG A:GLU268 3.6 40.5 1.0 CG A:ASP267 3.8 40.3 1.0 N A:GLY439 3.8 38.5 1.0 HG3 A:GLU268 3.9 48.6 1.0 MG A:MG601 3.9 32.7 1.0 H A:GLY439 4.0 46.2 1.0 O2B A:ADP603 4.0 40.4 1.0 C A:GLY439 4.2 38.6 1.0 CD2 A:LEU192 4.2 33.3 1.0 HD13 A:LEU192 4.2 32.0 1.0 CD1 A:LEU192 4.2 26.6 1.0 HD22 A:LEU192 4.2 39.9 1.0 HE2 A:LYS158 4.2 55.6 1.0 OE1 A:GLU268 4.2 52.8 1.0 O A:GLY439 4.4 44.1 1.0 H A:GLU268 4.6 53.1 1.0 C A:ARG438 4.7 38.3 1.0 O3B A:ADP603 4.8 42.8 1.0 HB3 A:ARG438 4.8 58.1 1.0 CG A:LEU192 4.8 30.8 1.0 HE3 A:LYS158 4.9 55.6 1.0 PB A:ADP603 4.9 35.2 1.0 HD23 A:LEU192 5.0 39.9 1.0 N A:GLU268 5.0 44.2 1.0 HD12 A:LEU192 5.0 32.0 1.0 CE A:LYS158 5.0 46.3 1.0

Fluorine binding site 2 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssdna 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 Ssdna and Adp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:30.9 occ:1.00 F2 A:BEF602 0.0 30.9 1.0 BE A:BEF602 1.6 34.2 1.0 F3 A:BEF602 2.5 36.1 1.0 O2B A:ADP603 2.5 40.4 1.0 F1 A:BEF602 2.6 47.7 1.0 OD2 A:ASP267 3.0 43.1 1.0 OD1 A:ASP267 3.2 39.8 1.0 HG1 A:THR159 3.2 42.3 1.0 OG1 A:THR159 3.4 35.2 1.0 CG A:ASP267 3.4 40.3 1.0 HB2 A:LYS158 3.5 47.4 1.0 HE2 A:LYS158 3.6 55.6 1.0 PB A:ADP603 4.0 35.2 1.0 HB3 A:LYS158 4.0 47.4 1.0 HE2 A:PHE162 4.1 37.3 1.0 HA A:THR159 4.2 42.6 1.0 CB A:LYS158 4.2 39.5 1.0 HD11 A:LEU192 4.2 32.0 1.0 N A:THR159 4.3 37.5 1.0 H A:THR159 4.3 45.0 1.0 HA2 A:GLY439 4.4 50.6 1.0 OE2 A:GLU268 4.5 49.6 1.0 CB A:THR159 4.5 31.2 1.0 CA A:THR159 4.5 35.5 1.0 O3B A:ADP603 4.6 42.8 1.0 O2A A:ADP603 4.6 41.5 1.0 C A:LYS158 4.6 40.2 1.0 CE A:LYS158 4.6 46.3 1.0 HA3 A:GLY439 4.7 50.6 1.0 O1B A:ADP603 4.7 35.6 1.0 MG A:MG601 4.8 32.7 1.0 HZ A:PHE162 4.8 38.8 1.0 O1A A:ADP603 4.8 48.0 1.0 HD11 A:ILE196 4.9 28.0 1.0 HE3 A:LYS158 4.9 55.6 1.0 H A:LYS158 4.9 44.1 1.0 HG2 A:GLU268 4.9 48.6 1.0 CA A:LYS158 4.9 34.2 1.0 HG22 A:THR159 4.9 37.6 1.0 CB A:ASP267 4.9 33.3 1.0 CE2 A:PHE162 4.9 31.1 1.0 O3A A:ADP603 4.9 36.0 1.0 HD21 A:LEU192 4.9 39.9 1.0 PA A:ADP603 5.0 34.8 1.0

Fluorine binding site 3 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssdna 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 Ssdna and Adp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:36.1 occ:1.00 F3 A:BEF602 0.0 36.1 1.0 BE A:BEF602 1.5 34.2 1.0 HA2 A:GLY439 2.5 50.6 1.0 F2 A:BEF602 2.5 30.9 1.0 F1 A:BEF602 2.5 47.7 1.0 O2B A:ADP603 2.5 40.4 1.0 O A:GLY439 2.9 44.1 1.0 O2A A:ADP603 3.1 41.5 1.0 HH22 A:ARG469 3.2 54.5 1.0 CA A:GLY439 3.2 42.1 1.0 O3B A:ADP603 3.2 42.8 1.0 HA3 A:GLY439 3.3 50.6 1.0 PB A:ADP603 3.4 35.2 1.0 C A:GLY439 3.5 38.6 1.0 MG A:MG601 3.6 32.7 1.0 HD11 A:LEU192 3.7 32.0 1.0 HG1 A:THR159 3.8 42.3 1.0 NH2 A:ARG469 3.8 45.4 1.0 HH21 A:ARG469 4.0 54.5 1.0 OG1 A:THR159 4.1 35.2 1.0 HE22 A:GLN195 4.1 32.9 1.0 PA A:ADP603 4.1 34.8 1.0 O3A A:ADP603 4.2 36.0 1.0 HH12 A:ARG466 4.3 51.0 1.0 HE21 A:GLN195 4.3 32.9 1.0 HD13 A:LEU192 4.4 32.0 1.0 OE2 A:GLU268 4.4 49.6 1.0 CD1 A:LEU192 4.4 26.6 1.0 N A:GLY439 4.5 38.5 1.0 NE2 A:GLN195 4.5 27.4 1.0 H A:GLY439 4.6 46.2 1.0 HE2 A:LYS158 4.6 55.6 1.0 OD2 A:ASP267 4.6 43.1 1.0 O1A A:ADP603 4.7 48.0 1.0 O1B A:ADP603 4.7 35.6 1.0 HH12 A:ARG469 4.7 57.0 1.0 HB2 A:LYS158 4.7 47.4 1.0 HD12 A:LEU192 4.8 32.0 1.0 N A:MET440 4.8 36.0 1.0 CZ A:ARG469 4.9 43.5 1.0 HB2 A:ASP441 4.9 38.7 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