Fluorine in PDB 7jl0: Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)

All present enzymatic activity of Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer):
3.6.4.13;

The structure of Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer) also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer) (pdb code 7jl0). 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 MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer), PDB code: 7jl0:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)


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 MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1103 b:43.8 occ:1.00 F1 A:ALF1103 0.0 43.8 1.0 AL A:ALF1103 1.8 43.8 1.0 O1B A:ADP1102 2.1 48.0 1.0 MG A:MG1104 2.1 24.6 1.0 F4 A:ALF1103 2.5 43.8 1.0 F3 A:ALF1103 2.6 43.8 1.0 PB A:ADP1102 3.1 48.0 1.0 O2B A:ADP1102 3.3 48.0 1.0 F2 A:ALF1103 3.6 43.8 1.0 CA A:GLY795 3.9 42.1 1.0 NH1 A:ARG822 4.0 48.5 1.0 O3B A:ADP1102 4.1 48.0 1.0 OE2 A:GLU444 4.2 48.5 1.0 N A:GLY795 4.3 42.1 1.0 O3A A:ADP1102 4.3 48.0 1.0 O A:GLY795 4.4 42.1 1.0 NH2 A:ARG822 4.4 48.5 1.0 C A:GLY795 4.5 42.1 1.0 O1A A:ADP1102 4.5 48.0 1.0 CZ A:ARG822 4.7 48.5 1.0 OD2 A:ASP443 4.9 48.5 1.0 PA A:ADP1102 4.9 48.0 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)


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 MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1103 b:43.8 occ:1.00 F2 A:ALF1103 0.0 43.8 1.0 AL A:ALF1103 1.8 43.8 1.0 F3 A:ALF1103 2.5 43.8 1.0 F4 A:ALF1103 2.6 43.8 1.0 O2B A:ADP1102 2.6 48.0 1.0 O3B A:ADP1102 2.9 48.0 1.0 PB A:ADP1102 3.0 48.0 1.0 NZ A:LYS335 3.2 48.5 1.0 CE A:LYS335 3.3 48.5 1.0 F1 A:ALF1103 3.6 43.8 1.0 O1B A:ADP1102 3.6 48.0 1.0 CG2 A:THR331 3.9 48.5 1.0 CB A:ALA489 4.0 48.5 1.0 MG A:MG1104 4.2 24.6 1.0 NH2 A:ARG822 4.2 48.5 1.0 CA A:THR331 4.3 48.5 1.0 NE2 A:GLN818 4.4 48.5 1.0 CB A:THR331 4.5 48.5 1.0 O3A A:ADP1102 4.5 48.0 1.0 CD A:LYS335 4.8 48.5 1.0 O A:THR488 5.0 48.5 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)


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 MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1103 b:43.8 occ:1.00 F3 A:ALF1103 0.0 43.8 1.0 AL A:ALF1103 1.8 43.8 1.0 NH2 A:ARG822 2.2 48.5 1.0 O2B A:ADP1102 2.2 48.0 1.0 F2 A:ALF1103 2.5 43.8 1.0 F1 A:ALF1103 2.6 43.8 1.0 CZ A:ARG822 3.0 48.5 1.0 NH1 A:ARG822 3.1 48.5 1.0 PB A:ADP1102 3.2 48.0 1.0 O1B A:ADP1102 3.3 48.0 1.0 F4 A:ALF1103 3.6 43.8 1.0 NE2 A:GLN818 3.8 48.5 1.0 O3B A:ADP1102 4.1 48.0 1.0 CG2 A:THR331 4.1 48.5 1.0 NE A:ARG822 4.2 48.5 1.0 MG A:MG1104 4.4 24.6 1.0 O3A A:ADP1102 4.4 48.0 1.0 N A:GLY795 4.6 42.1 1.0 CB A:THR331 4.6 48.5 1.0 NH2 A:ARG824 4.7 48.5 1.0 CA A:GLY795 4.9 42.1 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer)


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 MDA5-Dsrna in Complex with TRIM65 Pspry Domain (Monomer) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1103 b:43.8 occ:1.00 F4 A:ALF1103 0.0 43.8 1.0 AL A:ALF1103 1.8 43.8 1.0 MG A:MG1104 1.9 24.6 1.0 F1 A:ALF1103 2.5 43.8 1.0 F2 A:ALF1103 2.6 43.8 1.0 O1B A:ADP1102 2.6 48.0 1.0 O3B A:ADP1102 2.9 48.0 1.0 PB A:ADP1102 3.0 48.0 1.0 F3 A:ALF1103 3.6 43.8 1.0 O2B A:ADP1102 3.6 48.0 1.0 CE A:LYS335 3.6 48.5 1.0 OD1 A:ASP443 4.2 48.5 1.0 NZ A:LYS335 4.3 48.5 1.0 O3A A:ADP1102 4.5 48.0 1.0 CB A:LYS335 4.7 48.5 1.0 O2A A:ADP1102 4.7 48.0 1.0 OD2 A:ASP443 4.8 48.5 1.0 CD A:LYS335 4.8 48.5 1.0 CG A:ASP443 4.9 48.5 1.0 CG A:GLU444 4.9 48.5 1.0

K.Kato, S.Ahmad, Z.Zhu, J.M.Young, X.Mu, S.Park, H.S.Malik, S.Hur. Structural Analysis of Rig-I-Like Receptors Reveals Ancient Rules of Engagement Between Diverse Rna Helicases and Trim Ubiquitin Ligases Mol.Cell 2020.
ISSN: ISSN 1097-2765