Fluorine in PDB 9mx5: Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State

The structure of Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Aluminium	(Al)	1 atom

The binding sites of Fluorine atom in the Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State (pdb code 9mx5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State, PDB code: 9mx5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:102.1 occ:1.00 F1 A:AF3701 0.0 102.1 1.0 AL A:AF3701 1.6 112.7 1.0 O3B A:ADP702 2.2 96.6 1.0 F3 A:AF3701 2.8 115.8 1.0 F2 A:AF3701 2.8 99.5 1.0 NZ A:LYS37 3.0 91.5 1.0 O1B A:ADP702 3.0 96.3 1.0 PB A:ADP702 3.1 95.3 1.0 CE A:LYS37 3.3 90.7 1.0 CA A:THR33 3.8 90.1 1.0 N A:GLY34 4.0 94.8 1.0 O2B A:ADP702 4.1 94.9 1.0 O3A A:ADP702 4.2 108.3 1.0 CB A:THR33 4.4 83.9 1.0 O A:GLY32 4.5 91.8 1.0 C A:THR33 4.5 94.8 1.0 N A:THR33 4.7 89.3 1.0 MG A:MG703 4.7 83.0 1.0 CD A:LYS37 4.8 86.2 1.0 CB A:ALA176 4.9 92.0 1.0 C A:GLY32 4.9 91.5 1.0 CG2 A:THR33 5.0 80.7 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:99.5 occ:1.00 F2 A:AF3701 0.0 99.5 1.0 AL A:AF3701 1.6 112.7 1.0 F1 A:AF3701 2.8 102.1 1.0 F3 A:AF3701 2.8 115.8 1.0 NH2 A:ARG478 3.0 92.8 1.0 NH2 A:ARG480 3.6 101.7 1.0 O1B A:ADP702 3.7 96.3 1.0 O3B A:ADP702 4.1 96.6 1.0 CA A:GLY451 4.2 96.4 1.0 CB A:THR33 4.2 83.9 1.0 CZ A:ARG478 4.2 89.5 1.0 OE1 A:GLN474 4.3 106.2 1.0 PB A:ADP702 4.5 95.3 1.0 N A:GLY451 4.6 89.9 1.0 CA A:THR33 4.6 90.1 1.0 NH1 A:ARG478 4.7 87.5 1.0 CG2 A:THR33 4.8 80.7 1.0 C A:GLY451 4.8 100.1 1.0 O3A A:ADP702 4.9 108.3 1.0 N A:GLY34 4.9 94.8 1.0 O A:GLY451 5.0 98.8 1.0 CZ A:ARG480 5.0 106.1 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of Ancestral Dicer Helicase Bound to 27-Bp Dsrna in Internally-Bound Transition State within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:115.8 occ:1.00 F3 A:AF3701 0.0 115.8 1.0 AL A:AF3701 1.6 112.7 1.0 O3B A:ADP702 2.4 96.6 1.0 MG A:MG703 2.6 83.0 1.0 F1 A:AF3701 2.8 102.1 1.0 F2 A:AF3701 2.8 99.5 1.0 O3A A:ADP702 2.9 108.3 1.0 PB A:ADP702 3.0 95.3 1.0 O1B A:ADP702 3.3 96.3 1.0 O A:GLY451 4.2 98.8 1.0 PA A:ADP702 4.4 113.6 1.0 CA A:GLY451 4.4 96.4 1.0 O2B A:ADP702 4.5 94.9 1.0 OE2 A:GLU143 4.7 111.1 1.0 NH2 A:ARG480 4.7 101.7 1.0 C A:GLY451 4.7 100.1 1.0 O1A A:ADP702 4.7 108.8 1.0

A.M.Aderounmu, J.Maus-Conn, C.D.Consalvo, P.S.Shen, B.L.Bass. Biochemical and Structural Basis of Dicer Helicase Function Unveiled By Resurrecting Ancient Proteins. Biorxiv 2025.
ISSN: ISSN 2692-8205
PubMed: 39990435
DOI: 10.1101/2025.02.15.638221