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Fluorine in PDB 9f2l: Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist

Enzymatic activity of Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist

All present enzymatic activity of Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist:
3.6.4.13;

Other elements in 9f2l:

The structure of Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Aluminium (Al) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist (pdb code 9f2l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist, PDB code: 9f2l:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 9f2l

Go back to Fluorine Binding Sites List in 9f2l
Fluorine binding site 1 out of 4 in the Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist


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 the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:132.9
occ:1.00
F1 A:ALF1103 0.0 132.9 1.0
AL A:ALF1103 1.8 132.9 1.0
F4 A:ALF1103 2.5 132.9 1.0
F3 A:ALF1103 2.5 132.9 1.0
O3B A:ADP1102 2.6 122.1 1.0
O2B A:ADP1102 3.2 122.1 1.0
PB A:ADP1102 3.3 122.1 1.0
F2 A:ALF1103 3.6 132.9 1.0
O3A A:ADP1102 3.9 122.1 1.0
HH22 A:ARG822 4.0 109.5 1.0
H A:GLY333 4.2 119.9 1.0
HZ2 A:LYS336 4.5 107.5 1.0
O2A A:ADP1102 4.6 122.1 1.0
NH2 A:ARG822 4.7 109.5 1.0
O1B A:ADP1102 4.8 122.1 1.0
HH21 A:ARG822 4.8 109.5 1.0
HA2 A:GLY333 4.9 119.9 1.0
PA A:ADP1102 4.9 122.1 1.0
HE2 A:LYS336 4.9 107.5 1.0
N A:GLY333 5.0 119.9 1.0

Fluorine binding site 2 out of 4 in 9f2l

Go back to Fluorine Binding Sites List in 9f2l
Fluorine binding site 2 out of 4 in the Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist


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 the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:132.9
occ:1.00
F2 A:ALF1103 0.0 132.9 1.0
HZ2 A:LYS336 1.8 107.5 1.0
AL A:ALF1103 1.8 132.9 1.0
HA A:THR332 2.4 118.2 1.0
F4 A:ALF1103 2.5 132.9 1.0
F3 A:ALF1103 2.6 132.9 1.0
NZ A:LYS336 2.6 107.5 1.0
O2B A:ADP1102 2.8 122.1 1.0
HZ1 A:LYS336 2.9 107.5 1.0
HZ3 A:LYS336 3.0 107.5 1.0
HB A:THR332 3.1 118.2 1.0
H A:GLY333 3.2 119.9 1.0
CA A:THR332 3.3 118.2 1.0
HG22 A:THR332 3.4 118.2 1.0
F1 A:ALF1103 3.6 132.9 1.0
CB A:THR332 3.6 118.2 1.0
CE A:LYS336 3.6 107.5 1.0
HE2 A:LYS336 3.7 107.5 1.0
HE3 A:LYS336 3.7 107.5 1.0
N A:GLY333 3.9 119.9 1.0
HB2 A:ALA490 3.9 105.0 1.0
CG2 A:THR332 3.9 118.2 1.0
PB A:ADP1102 4.0 122.1 1.0
C A:THR332 4.2 118.2 1.0
O A:PRO331 4.2 111.2 1.0
O3B A:ADP1102 4.2 122.1 1.0
N A:THR332 4.2 118.2 1.0
HG21 A:THR332 4.3 118.2 1.0
HE22 A:GLN818 4.3 108.8 1.0
C A:PRO331 4.6 111.2 1.0
HH21 A:ARG822 4.7 109.5 1.0
CB A:ALA490 4.7 105.0 1.0
O1B A:ADP1102 4.8 122.1 1.0
HG23 A:THR332 4.8 118.2 1.0
HB3 A:ALA490 4.8 105.0 1.0
H A:THR332 4.8 118.2 1.0
HG3 A:LYS336 4.9 107.5 1.0
OG1 A:THR332 5.0 118.2 1.0
NE2 A:GLN818 5.0 108.8 1.0
CD A:LYS336 5.0 107.5 1.0

Fluorine binding site 3 out of 4 in 9f2l

Go back to Fluorine Binding Sites List in 9f2l
Fluorine binding site 3 out of 4 in the Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist


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 the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:132.9
occ:1.00
F3 A:ALF1103 0.0 132.9 1.0
AL A:ALF1103 1.8 132.9 1.0
F1 A:ALF1103 2.5 132.9 1.0
F2 A:ALF1103 2.6 132.9 1.0
HB A:THR332 2.6 118.2 1.0
H A:GLY333 2.7 119.9 1.0
O2B A:ADP1102 2.7 122.1 1.0
HH22 A:ARG822 2.9 109.5 1.0
HH21 A:ARG822 2.9 109.5 1.0
N A:GLY333 3.2 119.9 1.0
HA A:THR332 3.2 118.2 1.0
NH2 A:ARG822 3.3 109.5 1.0
CB A:THR332 3.5 118.2 1.0
F4 A:ALF1103 3.6 132.9 1.0
CA A:THR332 3.7 118.2 1.0
C A:THR332 3.8 118.2 1.0
PB A:ADP1102 3.9 122.1 1.0
HA2 A:GLY333 3.9 119.9 1.0
HZ2 A:LYS336 4.0 107.5 1.0
CA A:GLY333 4.1 119.9 1.0
O3B A:ADP1102 4.1 122.1 1.0
OG1 A:THR332 4.3 118.2 1.0
O3A A:ADP1102 4.3 122.1 1.0
HA3 A:GLY333 4.3 119.9 1.0
HG1 A:THR332 4.5 118.2 1.0
HG22 A:THR332 4.5 118.2 1.0
CG2 A:THR332 4.5 118.2 1.0
HG21 A:THR332 4.6 118.2 1.0
CZ A:ARG822 4.6 109.5 1.0
HZ1 A:LYS336 4.6 107.5 1.0
NZ A:LYS336 4.7 107.5 1.0
O A:THR332 4.9 118.2 1.0

Fluorine binding site 4 out of 4 in 9f2l

Go back to Fluorine Binding Sites List in 9f2l
Fluorine binding site 4 out of 4 in the Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of the I923V MDA5-Dsrna Filament with Adp-ALF4 Bound and 73-Degree Helical Twist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1103

b:132.9
occ:1.00
F4 A:ALF1103 0.0 132.9 1.0
AL A:ALF1103 1.8 132.9 1.0
F1 A:ALF1103 2.5 132.9 1.0
F2 A:ALF1103 2.5 132.9 1.0
HZ2 A:LYS336 2.8 107.5 1.0
O3B A:ADP1102 2.8 122.1 1.0
HE2 A:LYS336 2.8 107.5 1.0
O2B A:ADP1102 3.2 122.1 1.0
CE A:LYS336 3.4 107.5 1.0
NZ A:LYS336 3.4 107.5 1.0
PB A:ADP1102 3.4 122.1 1.0
HE3 A:LYS336 3.5 107.5 1.0
F3 A:ALF1103 3.6 132.9 1.0
HZ1 A:LYS336 3.6 107.5 1.0
HZ3 A:LYS336 4.1 107.5 1.0
O1B A:ADP1102 4.3 122.1 1.0
HB2 A:LYS336 4.5 107.5 1.0
H A:GLY333 4.6 119.9 1.0
OD1 A:ASP444 4.7 95.2 1.0
HA A:THR332 4.7 118.2 1.0
CD A:LYS336 4.8 107.5 1.0
O3A A:ADP1102 4.8 122.1 1.0
HG3 A:LYS336 4.9 107.5 1.0

Reference:

R.Singh, A.Herrero Del Valle, J.D.Joiner, M.Zwaagstra, B.J.Ferguson, F.J.M.Van Kuppeveld, Y.Modis. Molecular Basis of Autoimmune Disease Protection By MDA5 Variants Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.10.03.616466
Page generated: Wed Jul 16 11:38:05 2025

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