Fluorine in PDB 4tz6: Dead-Box Helicase MSS116 Bound to Ssrna and Udp-Bef

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

The structure of Dead-Box Helicase MSS116 Bound to Ssrna and Udp-Bef, PDB code: 4tz6 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)	47.21 / 3.21
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.757, 126.506, 55.510, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27

The structure of Dead-Box Helicase MSS116 Bound to Ssrna and Udp-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 Udp-Bef (pdb code 4tz6). 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 Udp-Bef, PDB code: 4tz6:
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 Udp-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 Udp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:79.5 occ:1.00 F1 A:BEF601 0.0 79.5 1.0 BE A:BEF601 1.5 74.1 1.0 F3 A:BEF601 2.5 59.0 1.0 F2 A:BEF601 2.5 81.1 1.0 NZ A:LYS158 2.7 86.7 1.0 HG22 A:THR154 2.7 91.2 1.0 HA A:THR154 3.0 85.4 1.0 HB2 A:ALA306 3.1 87.4 1.0 HH22 A:ARG466 3.2 79.4 1.0 CE A:LYS158 3.4 79.4 1.0 CG2 A:THR154 3.7 76.0 1.0 OE2 A:GLU268 3.7 66.5 1.0 O3B A:UDP602 3.7 51.3 1.0 O1B A:UDP602 3.8 85.3 1.0 CA A:THR154 3.9 71.2 1.0 H A:GLY155 3.9 83.7 1.0 HB3 A:ALA306 3.9 87.4 1.0 CB A:ALA306 4.0 72.8 1.0 O2B A:UDP602 4.0 61.9 1.0 H A:ALA306 4.0 79.0 1.0 HG23 A:THR154 4.0 91.2 1.0 NH2 A:ARG466 4.0 66.2 1.0 PB A:UDP602 4.0 59.1 1.0 HB A:THR154 4.1 98.3 1.0 CB A:THR154 4.1 81.9 1.0 HH12 A:ARG469 4.1 71.3 1.0 HE1 A:HIS462 4.3 80.3 1.0 HG21 A:THR154 4.3 91.2 1.0 MG A:MG603 4.3 39.3 1.0 HH21 A:ARG466 4.4 79.4 1.0 H A:GLY439 4.4 55.9 1.0 ND1 A:HIS462 4.4 66.5 1.0 HA2 A:GLY439 4.4 67.2 1.0 HH22 A:ARG469 4.4 79.1 1.0 HH12 A:ARG466 4.5 71.6 1.0 N A:ALA306 4.5 65.8 1.0 CD A:GLU268 4.6 63.6 1.0 HB1 A:ALA306 4.6 87.4 1.0 OE1 A:GLU268 4.6 68.9 1.0 N A:GLY155 4.6 69.7 1.0 N A:THR154 4.6 70.2 1.0 CD A:LYS158 4.7 47.5 1.0 CE1 A:HIS462 4.7 66.9 1.0 CA A:ALA306 4.8 66.7 1.0 C A:THR154 4.8 74.9 1.0 HA A:SER305 4.9 77.7 1.0 O A:LYS153 4.9 73.5 1.0

Fluorine binding site 2 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssrna and Udp-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 Udp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:81.1 occ:1.00 F2 A:BEF601 0.0 81.1 1.0 BE A:BEF601 1.6 74.1 1.0 MG A:MG603 2.2 39.3 1.0 F3 A:BEF601 2.5 59.0 1.0 HA2 A:GLY439 2.5 67.2 1.0 F1 A:BEF601 2.5 79.5 1.0 O2B A:UDP602 2.6 61.9 1.0 OE2 A:GLU268 2.8 66.5 1.0 O1B A:UDP602 3.1 85.3 1.0 PB A:UDP602 3.4 59.1 1.0 CA A:GLY439 3.4 56.0 1.0 H A:GLY439 3.6 55.9 1.0 HH22 A:ARG469 3.7 79.1 1.0 HH12 A:ARG466 3.8 71.6 1.0 HA3 A:GLY439 3.9 67.2 1.0 HH22 A:ARG466 3.9 79.4 1.0 N A:GLY439 3.9 46.6 1.0 NZ A:LYS158 4.0 86.7 1.0 O3B A:UDP602 4.0 51.3 1.0 CD A:GLU268 4.1 63.6 1.0 O A:GLY439 4.1 54.5 1.0 C A:GLY439 4.3 49.6 1.0 O1A A:UDP602 4.4 77.6 1.0 HH12 A:ARG469 4.5 71.3 1.0 NH2 A:ARG469 4.5 65.9 1.0 CE A:LYS158 4.5 79.4 1.0 NH1 A:ARG466 4.6 59.6 1.0 NH2 A:ARG466 4.7 66.2 1.0 H A:GLY155 4.7 83.7 1.0 OE1 A:GLU268 4.8 68.9 1.0 O3A A:UDP602 4.8 67.1 1.0 HG2 A:GLU268 4.9 60.3 1.0 OD1 A:ASP267 4.9 54.8 1.0 HH21 A:ARG469 4.9 79.1 1.0 HA A:THR154 4.9 85.4 1.0 HG22 A:THR154 4.9 91.2 1.0 HD11 A:LEU192 5.0 52.7 1.0

Fluorine binding site 3 out of 3 in the Dead-Box Helicase MSS116 Bound to Ssrna and Udp-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 Udp-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:59.0 occ:1.00 F3 A:BEF601 0.0 59.0 1.0 BE A:BEF601 1.5 74.1 1.0 HH22 A:ARG466 2.0 79.4 1.0 HH12 A:ARG469 2.2 71.3 1.0 HH12 A:ARG466 2.2 71.6 1.0 F1 A:BEF601 2.5 79.5 1.0 F2 A:BEF601 2.5 81.1 1.0 HH22 A:ARG469 2.6 79.1 1.0 NH2 A:ARG466 2.7 66.2 1.0 O1B A:UDP602 2.8 85.3 1.0 NH1 A:ARG466 2.9 59.6 1.0 NH1 A:ARG469 2.9 59.4 1.0 CZ A:ARG466 3.2 57.2 1.0 NH2 A:ARG469 3.2 65.9 1.0 HA2 A:GLY439 3.3 67.2 1.0 H A:GLY155 3.3 83.7 1.0 H A:GLY439 3.4 55.9 1.0 HG22 A:THR154 3.4 91.2 1.0 HH21 A:ARG466 3.4 79.4 1.0 CZ A:ARG469 3.5 60.2 1.0 HH11 A:ARG469 3.6 71.3 1.0 HB A:THR154 3.6 98.3 1.0 HH11 A:ARG466 3.7 71.6 1.0 HA A:THR154 3.7 85.4 1.0 PB A:UDP602 3.9 59.1 1.0 CA A:GLY439 4.0 56.0 1.0 HH21 A:ARG469 4.0 79.1 1.0 N A:GLY439 4.0 46.6 1.0 N A:GLY155 4.1 69.7 1.0 O2B A:UDP602 4.1 61.9 1.0 CG2 A:THR154 4.1 76.0 1.0 CB A:THR154 4.1 81.9 1.0 O3B A:UDP602 4.3 51.3 1.0 CA A:THR154 4.3 71.2 1.0 O A:GLY439 4.3 54.5 1.0 C A:GLY439 4.4 49.6 1.0 HG21 A:THR154 4.4 91.2 1.0 OE2 A:GLU268 4.5 66.5 1.0 NE A:ARG466 4.5 41.4 1.0 MG A:MG603 4.6 39.3 1.0 HA2 A:GLY155 4.7 70.6 1.0 O1A A:UDP602 4.7 77.6 1.0 C A:THR154 4.7 74.9 1.0 NE A:ARG469 4.8 59.0 1.0 HA3 A:GLY439 4.8 67.2 1.0 O A:GLY465 4.9 58.6 1.0 HG23 A:THR154 4.9 91.2 1.0 HE A:ARG466 5.0 49.7 1.0 NZ A:LYS158 5.0 86.7 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