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

Other elements in 9mx5:

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

Fluorine Binding Sites:

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 9mx5

Go back to Fluorine Binding Sites List in 9mx5
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 9mx5

Go back to Fluorine Binding Sites List in 9mx5
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 9mx5

Go back to Fluorine Binding Sites List in 9mx5
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

Reference:

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
Page generated: Wed Jul 16 11:52:20 2025

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