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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4tyw:

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

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

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 4tyw

Go back to Fluorine Binding Sites List in 4tyw
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 4tyw

Go back to Fluorine Binding Sites List in 4tyw
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 4tyw

Go back to Fluorine Binding Sites List in 4tyw
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

Reference:

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
Page generated: Sun Dec 13 12:12:42 2020

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