Fluorine in PDB 6uv4: Crystal Structure of Apo Core Domain of Rna Helicase DDX17

All present enzymatic activity of Crystal Structure of Apo Core Domain of Rna Helicase DDX17:
3.6.4.13;

The structure of Crystal Structure of Apo Core Domain of Rna Helicase DDX17, PDB code: 6uv4 was solved by T.D.Ngo, A.C.Partin, Y.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.55 / 1.70
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.504, 62.504, 231.196, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.4

The structure of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17 (pdb code 6uv4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17, PDB code: 6uv4:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:6.3 occ:1.00 F1 A:BEF502 0.0 6.3 1.0 BE A:BEF502 1.5 6.3 1.0 MG A:MG503 1.9 6.0 1.0 F3 A:BEF502 2.5 6.0 1.0 O1B A:ADP501 2.5 4.6 1.0 F2 A:BEF502 2.5 6.7 1.0 O A:HOH728 2.8 4.9 1.0 O3B A:ADP501 2.9 4.3 1.0 O A:HOH695 2.9 5.0 1.0 O A:HOH744 3.0 5.1 1.0 PB A:ADP501 3.2 5.2 1.0 OE2 A:GLU247 3.3 8.2 1.0 O A:HOH784 3.4 6.1 1.0 CA A:GLY402 3.4 5.6 1.0 O A:HOH822 3.5 8.3 1.0 N A:GLY402 4.0 6.0 1.0 O A:HOH655 4.0 5.8 1.0 O A:GLY402 4.1 6.4 1.0 NH2 A:ARG432 4.1 6.2 1.0 C A:GLY402 4.2 5.7 1.0 O2B A:ADP501 4.4 5.2 1.0 NZ A:LYS142 4.4 5.4 1.0 O3A A:ADP501 4.4 5.2 1.0 CD A:GLU247 4.4 7.9 1.0 CE A:LYS142 4.5 5.2 1.0 NH1 A:ARG429 4.6 6.0 1.0 O2A A:ADP501 4.8 6.2 1.0 NH1 A:ARG432 4.9 6.3 1.0 OE1 A:GLU247 4.9 7.7 1.0 NH2 A:ARG429 4.9 5.0 1.0 CZ A:ARG432 5.0 6.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:6.7 occ:1.00 F2 A:BEF502 0.0 6.7 1.0 BE A:BEF502 1.6 6.3 1.0 F3 A:BEF502 2.4 6.0 1.0 O1B A:ADP501 2.4 4.6 1.0 F1 A:BEF502 2.5 6.3 1.0 NH1 A:ARG432 2.8 6.3 1.0 NH2 A:ARG429 3.0 5.0 1.0 NH1 A:ARG429 3.1 6.0 1.0 O A:HOH784 3.1 6.1 1.0 NH2 A:ARG432 3.2 6.2 1.0 CZ A:ARG429 3.4 6.3 1.0 CZ A:ARG432 3.4 6.9 1.0 N A:GLY139 3.6 4.8 1.0 CB A:THR138 3.6 6.5 1.0 CA A:THR138 3.7 4.3 1.0 CG2 A:THR138 3.8 6.5 1.0 PB A:ADP501 3.9 5.2 1.0 CA A:GLY402 4.1 5.6 1.0 N A:GLY402 4.1 6.0 1.0 C A:THR138 4.2 7.1 1.0 MG A:MG503 4.3 6.0 1.0 O3B A:ADP501 4.5 4.3 1.0 C A:GLY402 4.5 5.7 1.0 O A:HOH744 4.5 5.1 1.0 O A:GLY402 4.6 6.4 1.0 O A:HOH822 4.6 8.3 1.0 CA A:GLY139 4.6 6.2 1.0 O A:GLY428 4.7 7.3 1.0 O3A A:ADP501 4.7 5.2 1.0 NE A:ARG432 4.7 6.6 1.0 NE A:ARG429 4.8 5.9 1.0 NZ A:LYS142 4.9 5.4 1.0 OE2 A:GLU247 4.9 8.2 1.0 O2B A:ADP501 4.9 5.2 1.0 OG1 A:THR138 5.0 5.5 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:6.0 occ:1.00 F3 A:BEF502 0.0 6.0 1.0 BE A:BEF502 1.6 6.3 1.0 F2 A:BEF502 2.4 6.7 1.0 F1 A:BEF502 2.5 6.3 1.0 O1B A:ADP501 2.5 4.6 1.0 NZ A:LYS142 2.8 5.4 1.0 O A:HOH822 2.8 8.3 1.0 O A:HOH784 3.3 6.1 1.0 CA A:THR138 3.4 4.3 1.0 CE A:LYS142 3.4 5.2 1.0 PB A:ADP501 3.5 5.2 1.0 CG2 A:THR138 3.7 6.5 1.0 O A:HOH728 3.8 4.9 1.0 CB A:THR138 3.9 6.5 1.0 O2B A:ADP501 3.9 5.2 1.0 O3B A:ADP501 4.0 4.3 1.0 MG A:MG503 4.0 6.0 1.0 CB A:ALA278 4.0 7.3 1.0 N A:GLY139 4.0 4.8 1.0 N A:THR138 4.1 5.5 1.0 C A:THR138 4.3 7.1 1.0 O A:GLN137 4.4 6.8 1.0 OE2 A:GLU247 4.5 8.2 1.0 N A:ALA278 4.5 5.5 1.0 NH2 A:ARG429 4.6 5.0 1.0 C A:GLN137 4.6 5.3 1.0 CA A:ALA278 4.8 6.4 1.0 O A:ALA136 4.8 7.7 1.0 CD A:LYS142 4.9 6.2 1.0 ND1 A:HIS425 4.9 8.4 1.0 NH1 A:ARG432 4.9 6.3 1.0 CE1 A:HIS425 4.9 7.8 1.0 O3A A:ADP501 5.0 5.2 1.0

T.D.Ngo, A.C.Partin, Y.Nam. Rna Specificity and Autoregulation of DDX17, A Modulator of Microrna Biogenesis. Cell Rep V. 29 4024 2019.
ISSN: ESSN 2211-1247
PubMed: 31851931
DOI: 10.1016/J.CELREP.2019.11.059