Fluorine in PDB 5vhc: DHX36 with An N-Terminal Truncation Bound to Adp-BEF3

The structure of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3, PDB code: 5vhc was solved by M.Chen, A.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.50 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.878, 111.516, 62.966, 90.00, 110.67, 90.00
R / Rfree (%)	19.4 / 23.3

The structure of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 (pdb code 5vhc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3, PDB code: 5vhc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1102 b:48.5 occ:1.00 F1 D:BEF1102 0.0 48.5 1.0 BE D:BEF1102 1.5 45.4 1.0 MG D:MG1101 2.0 47.4 1.0 O3B D:ADP1103 2.4 41.3 1.0 F3 D:BEF1102 2.5 40.8 1.0 F2 D:BEF1102 2.6 50.1 1.0 OE1 D:GLU337 3.0 45.9 1.0 OE2 D:GLU337 3.4 61.3 1.0 PB D:ADP1103 3.4 40.3 1.0 O D:HOH1260 3.5 41.6 1.0 O1B D:ADP1103 3.5 41.0 1.0 CD D:GLU337 3.6 50.8 1.0 NH2 D:ARG607 3.6 67.8 1.0 CA D:SER559 3.7 48.8 1.0 N D:SER559 3.9 48.2 1.0 OG1 D:THR239 3.9 45.2 1.0 NH2 D:ARG604 4.3 39.8 1.0 O2B D:ADP1103 4.5 38.1 1.0 O2A D:ADP1103 4.5 41.5 1.0 O D:SER559 4.5 51.4 1.0 O3A D:ADP1103 4.6 41.3 1.0 CB D:SER559 4.6 45.0 1.0 C D:SER559 4.6 48.7 1.0 NH1 D:ARG604 4.8 46.8 1.0 OE1 D:GLN600 4.9 41.6 1.0 NZ D:LYS238 4.9 41.7 1.0 CZ D:ARG607 4.9 61.9 1.0 CE D:LYS238 4.9 47.2 1.0 OG D:SER559 5.0 47.7 1.0

Fluorine binding site 2 out of 3 in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1102 b:50.1 occ:1.00 F2 D:BEF1102 0.0 50.1 1.0 BE D:BEF1102 1.6 45.4 1.0 F3 D:BEF1102 2.5 40.8 1.0 O3B D:ADP1103 2.5 41.3 1.0 F1 D:BEF1102 2.6 48.5 1.0 NZ D:LYS238 2.9 41.7 1.0 O D:HOH1260 2.9 41.6 1.0 PB D:ADP1103 3.3 40.3 1.0 CB D:ALA369 3.3 46.1 1.0 CE D:LYS238 3.3 47.2 1.0 O2B D:ADP1103 3.4 38.1 1.0 CA D:THR234 3.6 40.5 1.0 MG D:MG1101 3.6 47.4 1.0 N D:GLY235 3.9 37.3 1.0 CG2 D:THR234 4.0 38.4 1.0 O1B D:ADP1103 4.0 41.0 1.0 O D:GLU233 4.1 50.3 1.0 CB D:THR234 4.3 37.8 1.0 C D:THR234 4.3 39.6 1.0 N D:THR234 4.3 47.0 1.0 N D:ALA369 4.3 42.2 1.0 CA D:ALA369 4.3 44.0 1.0 NH2 D:ARG607 4.5 67.8 1.0 C D:GLU233 4.6 49.5 1.0 O D:GLY232 4.7 44.2 1.0 OE2 D:GLU337 4.7 61.3 1.0 O3A D:ADP1103 4.7 41.3 1.0 CD D:LYS238 4.8 51.6 1.0 NH2 D:ARG604 4.8 39.8 1.0 OE1 D:GLN600 4.9 41.6 1.0 NE2 D:GLN600 5.0 42.8 1.0

Fluorine binding site 3 out of 3 in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1102 b:40.8 occ:1.00 F3 D:BEF1102 0.0 40.8 1.0 BE D:BEF1102 1.5 45.4 1.0 NH2 D:ARG607 2.3 67.8 1.0 O3B D:ADP1103 2.3 41.3 1.0 F2 D:BEF1102 2.5 50.1 1.0 F1 D:BEF1102 2.5 48.5 1.0 NH2 D:ARG604 2.8 39.8 1.0 N D:GLY235 3.4 37.3 1.0 CZ D:ARG607 3.5 61.9 1.0 CA D:THR234 3.6 40.5 1.0 CB D:THR234 3.6 37.8 1.0 CG2 D:THR234 3.6 38.4 1.0 CZ D:ARG604 3.7 43.4 1.0 PB D:ADP1103 3.8 40.3 1.0 NH1 D:ARG604 3.8 46.8 1.0 C D:THR234 3.9 39.6 1.0 NE D:ARG607 4.2 49.6 1.0 MG D:MG1101 4.3 47.4 1.0 O D:HOH1260 4.3 41.6 1.0 NH1 D:ARG607 4.3 69.0 1.0 CA D:GLY235 4.3 36.8 1.0 OE1 D:GLN600 4.4 41.6 1.0 O2B D:ADP1103 4.4 38.1 1.0 O3A D:ADP1103 4.5 41.3 1.0 N D:SER559 4.7 48.2 1.0 O1B D:ADP1103 4.8 41.0 1.0 CA D:SER559 4.8 48.8 1.0 N D:THR234 4.9 47.0 1.0 NE D:ARG604 4.9 43.5 1.0 O D:SER559 5.0 51.4 1.0 O D:GLY603 5.0 54.6 1.0

M.C.Chen, R.Tippana, N.A.Demeshkina, P.Murat, S.Balasubramanian, S.Myong, A.R.Ferre-D'amare. Structural Basis of G-Quadruplex Unfolding By the Deah/Rha Helicase DHX36. Nature V. 558 465 2018.
ISSN: ESSN 1476-4687
PubMed: 29899445
DOI: 10.1038/S41586-018-0209-9