Magnesium in PDB 7jl2: Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)

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

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

Fluorine	(F)	12 atoms
Aluminium	(Al)	3 atoms
Zinc	(Zn)	3 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) (pdb code 7jl2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer), PDB code: 7jl2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:59.3 occ:1.00 F4 A:ALF1103 1.9 73.5 1.0 F1 A:ALF1103 1.9 73.5 1.0 O1B A:ADP1102 1.9 73.6 1.0 AL A:ALF1103 2.5 73.5 1.0 PB A:ADP1102 3.4 73.6 1.0 O2B A:ADP1102 3.9 73.6 1.0 F3 A:ALF1103 3.9 73.5 1.0 F2 A:ALF1103 4.0 73.5 1.0 O3A A:ADP1102 4.1 73.6 1.0 CA A:GLY795 4.3 61.3 1.0 O1A A:ADP1102 4.3 73.6 1.0 O2A A:ADP1102 4.4 73.6 1.0 O3B A:ADP1102 4.4 73.6 1.0 OD2 A:ASP443 4.4 95.0 1.0 PA A:ADP1102 4.5 73.6 1.0 OE2 A:GLU444 4.7 95.0 1.0 O A:GLY795 4.7 61.3 1.0 NZ A:LYS335 4.8 95.0 1.0 CE A:LYS335 4.8 95.0 1.0 C A:GLY795 4.9 61.3 1.0 OD1 A:ASP443 4.9 95.0 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1104 b:87.2 occ:1.00 F4 C:ALF1103 1.9 88.8 1.0 F1 C:ALF1103 1.9 88.8 1.0 O1B C:ADP1102 1.9 85.8 1.0 AL C:ALF1103 2.5 88.8 1.0 PB C:ADP1102 3.4 85.8 1.0 O2B C:ADP1102 3.9 85.8 1.0 F3 C:ALF1103 3.9 88.8 1.0 F2 C:ALF1103 4.0 88.8 1.0 O3A C:ADP1102 4.1 85.8 1.0 CA C:GLY795 4.3 70.9 1.0 O1A C:ADP1102 4.3 85.8 1.0 O2A C:ADP1102 4.4 85.8 1.0 O3B C:ADP1102 4.4 85.8 1.0 OD2 C:ASP443 4.4 95.0 1.0 PA C:ADP1102 4.5 85.8 1.0 OE2 C:GLU444 4.7 95.0 1.0 O C:GLY795 4.7 70.9 1.0 NZ C:LYS335 4.8 95.0 1.0 CE C:LYS335 4.8 95.0 1.0 C C:GLY795 4.9 70.9 1.0 OD1 C:ASP443 4.9 95.0 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of MDA5-Dsrna Filament in Complex with TRIM65 Pspry Domain (Trimer) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1104 b:66.8 occ:1.00 F4 E:ALF1103 1.9 75.0 1.0 F1 E:ALF1103 1.9 75.0 1.0 O1B E:ADP1102 1.9 76.2 1.0 AL E:ALF1103 2.5 75.0 1.0 PB E:ADP1102 3.4 76.2 1.0 O2B E:ADP1102 3.9 76.2 1.0 F3 E:ALF1103 3.9 75.0 1.0 F2 E:ALF1103 4.0 75.0 1.0 O3A E:ADP1102 4.1 76.2 1.0 CA E:GLY795 4.3 61.8 1.0 O1A E:ADP1102 4.3 76.2 1.0 O2A E:ADP1102 4.4 76.2 1.0 O3B E:ADP1102 4.4 76.2 1.0 OD2 E:ASP443 4.4 95.0 1.0 PA E:ADP1102 4.5 76.2 1.0 OE2 E:GLU444 4.7 95.0 1.0 O E:GLY795 4.7 61.8 1.0 NZ E:LYS335 4.8 95.0 1.0 CE E:LYS335 4.8 95.0 1.0 C E:GLY795 4.9 61.8 1.0 OD1 E:ASP443 4.9 95.0 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