Fluorine in PDB 5vhd: DHX36 with An N-Terminal Truncation Bound to Adp-ALF4

The structure of DHX36 with An N-Terminal Truncation Bound to Adp-ALF4, PDB code: 5vhd 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)	46.73 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.030, 112.500, 63.180, 90.00, 110.33, 90.00
R / Rfree (%)	17.3 / 21.3

The structure of DHX36 with An N-Terminal Truncation Bound to Adp-ALF4 also contains other interesting chemical elements:

Aluminium

(Al)

1 atom

The binding sites of Fluorine atom in the DHX36 with An N-Terminal Truncation Bound to Adp-ALF4 (pdb code 5vhd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the DHX36 with An N-Terminal Truncation Bound to Adp-ALF4, PDB code: 5vhd:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the DHX36 with An N-Terminal Truncation Bound to Adp-ALF4


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-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1102 b:0.8 occ:1.00 F1 D:ALF1102 0.0 0.8 1.0 AL D:ALF1102 1.8 90.6 1.0 O D:HOH1211 2.3 57.7 1.0 OE1 D:GLU337 2.5 63.6 1.0 F4 D:ALF1102 2.5 85.0 1.0 F3 D:ALF1102 2.5 88.7 1.0 O3B D:ADP1101 3.3 84.3 1.0 CD D:GLU337 3.3 49.0 1.0 O1B D:ADP1101 3.5 72.4 1.0 F2 D:ALF1102 3.6 90.0 1.0 OE2 D:GLU337 3.6 42.2 1.0 N D:SER559 3.8 59.1 1.0 OG1 D:THR239 3.8 33.7 1.0 PB D:ADP1101 3.9 77.5 1.0 CA D:SER559 3.9 55.8 1.0 NH2 D:ARG607 4.4 77.1 1.0 NZ D:LYS238 4.4 79.0 1.0 OG D:SER559 4.4 67.6 1.0 CG D:GLU337 4.5 38.1 1.0 NH2 D:ARG604 4.6 36.8 1.0 OE1 D:GLN600 4.7 41.2 1.0 OD2 D:ASP336 4.7 59.9 1.0 O2B D:ADP1101 4.7 78.7 1.0 CB D:SER559 4.8 55.7 1.0 CE D:LYS238 4.9 76.6 1.0 C D:SER559 4.9 49.9 1.0 OD1 D:ASP336 4.9 62.5 1.0 O2A D:ADP1101 4.9 85.8 1.0 O D:SER559 4.9 54.2 1.0 C D:THR558 5.0 56.0 1.0

Fluorine binding site 2 out of 4 in the DHX36 with An N-Terminal Truncation Bound to Adp-ALF4


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-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1102 b:90.0 occ:1.00 F2 D:ALF1102 0.0 90.0 1.0 AL D:ALF1102 1.8 90.6 1.0 NH2 D:ARG607 2.4 77.1 1.0 F3 D:ALF1102 2.5 88.7 1.0 F4 D:ALF1102 2.5 85.0 1.0 NH2 D:ARG604 2.7 36.8 1.0 O3B D:ADP1101 2.7 84.3 1.0 N D:GLY235 3.0 43.9 1.0 CA D:THR234 3.2 57.0 1.0 CB D:THR234 3.3 52.2 1.0 CG2 D:THR234 3.4 55.7 1.0 C D:THR234 3.5 54.2 1.0 CZ D:ARG607 3.6 67.7 1.0 F1 D:ALF1102 3.6 0.8 1.0 CZ D:ARG604 3.7 43.9 1.0 NH1 D:ARG604 4.1 41.5 1.0 CA D:GLY235 4.1 50.4 1.0 PB D:ADP1101 4.2 77.5 1.0 OE1 D:GLN600 4.2 41.2 1.0 NE D:ARG607 4.3 60.3 1.0 NH1 D:ARG607 4.4 69.3 1.0 N D:THR234 4.5 64.6 1.0 CB D:ALA369 4.6 53.3 1.0 O D:THR234 4.7 56.8 1.0 OG1 D:THR234 4.7 62.5 1.0 O2B D:ADP1101 4.7 78.7 1.0 O D:HOH1211 4.7 57.7 1.0 O D:GLY603 4.8 44.6 1.0 NE D:ARG604 4.8 53.4 1.0 O D:GLU233 5.0 57.9 1.0

Fluorine binding site 3 out of 4 in the DHX36 with An N-Terminal Truncation Bound to Adp-ALF4


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-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1102 b:88.7 occ:1.00 F3 D:ALF1102 0.0 88.7 1.0 AL D:ALF1102 1.8 90.6 1.0 NH2 D:ARG607 2.5 77.1 1.0 F2 D:ALF1102 2.5 90.0 1.0 F1 D:ALF1102 2.5 0.8 1.0 NH2 D:ARG604 2.5 36.8 1.0 NH1 D:ARG604 2.7 41.5 1.0 N D:SER559 2.8 59.1 1.0 CZ D:ARG604 3.0 43.9 1.0 O D:HOH1211 3.1 57.7 1.0 CA D:SER559 3.2 55.8 1.0 O3B D:ADP1101 3.3 84.3 1.0 F4 D:ALF1102 3.6 85.0 1.0 C D:SER559 3.6 49.9 1.0 O D:SER559 3.6 54.2 1.0 CZ D:ARG607 3.7 67.7 1.0 OE1 D:GLU337 3.8 63.6 1.0 C D:THR558 3.8 56.0 1.0 OE1 D:GLN600 4.2 41.2 1.0 CA D:THR558 4.2 51.9 1.0 NE D:ARG604 4.3 53.4 1.0 NE D:ARG607 4.4 60.3 1.0 N D:ILE560 4.5 44.9 1.0 NH1 D:ARG607 4.5 69.3 1.0 PB D:ADP1101 4.5 77.5 1.0 O2A D:ADP1101 4.6 85.8 1.0 CB D:SER559 4.6 55.7 1.0 O D:ILE560 4.7 45.9 1.0 O1B D:ADP1101 4.7 72.4 1.0 O D:THR558 4.7 55.3 1.0 CD D:GLU337 4.9 49.0 1.0 CB D:THR558 4.9 51.2 1.0 OG D:SER559 5.0 67.6 1.0

Fluorine binding site 4 out of 4 in the DHX36 with An N-Terminal Truncation Bound to Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of DHX36 with An N-Terminal Truncation Bound to Adp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1102 b:85.0 occ:1.00 F4 D:ALF1102 0.0 85.0 1.0 AL D:ALF1102 1.8 90.6 1.0 F1 D:ALF1102 2.5 0.8 1.0 F2 D:ALF1102 2.5 90.0 1.0 O3B D:ADP1101 2.8 84.3 1.0 CB D:ALA369 3.1 53.3 1.0 PB D:ADP1101 3.4 77.5 1.0 NZ D:LYS238 3.5 79.0 1.0 O2B D:ADP1101 3.5 78.7 1.0 F3 D:ALF1102 3.6 88.7 1.0 CE D:LYS238 3.7 76.6 1.0 CA D:THR234 3.9 57.0 1.0 O1B D:ADP1101 3.9 72.4 1.0 N D:GLY235 4.0 43.9 1.0 O D:HOH1211 4.2 57.7 1.0 O D:GLU233 4.3 57.9 1.0 CA D:ALA369 4.3 45.7 1.0 CG2 D:THR234 4.3 55.7 1.0 NH2 D:ARG607 4.3 77.1 1.0 N D:ALA369 4.4 51.6 1.0 C D:THR234 4.5 54.2 1.0 CB D:THR234 4.6 52.2 1.0 OE1 D:GLN600 4.6 41.2 1.0 N D:THR234 4.6 64.6 1.0 NH2 D:ARG604 4.7 36.8 1.0 OE1 D:GLU337 4.7 63.6 1.0 NE2 D:GLN600 4.7 41.9 1.0 C D:GLU233 4.8 61.2 1.0 O3A D:ADP1101 4.9 88.5 1.0 OE2 D:GLU337 4.9 42.2 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