Magnesium in PDB 7jl3: Cryo-Em Structure of Rig-I:Dsrna Filament in Complex with Riplet Pryspry Domain (Trimer)

All present enzymatic activity of Cryo-Em Structure of Rig-I:Dsrna Filament in Complex with Riplet Pryspry Domain (Trimer):
2.3.2.27; 3.6.4.13;

The structure of Cryo-Em Structure of Rig-I:Dsrna Filament in Complex with Riplet Pryspry 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 Rig-I:Dsrna Filament in Complex with Riplet Pryspry Domain (Trimer) (pdb code 7jl3). 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 Rig-I:Dsrna Filament in Complex with Riplet Pryspry Domain (Trimer), PDB code: 7jl3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of Rig-I:Dsrna Filament in Complex with Riplet Pryspry 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 Rig-I:Dsrna Filament in Complex with Riplet Pryspry Domain (Trimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:82.8 occ:1.00 O1B A:ADP2001 2.0 82.8 1.0 F4 A:ALF2002 2.0 82.8 1.0 F1 A:ALF2002 2.1 82.8 1.0 AL A:ALF2002 2.9 82.8 1.0 O1A A:ADP2001 3.4 82.8 1.0 PB A:ADP2001 3.5 82.8 1.0 OE2 A:GLU373 3.7 46.6 1.0 PA A:ADP2001 3.9 82.8 1.0 O2A A:ADP2001 4.0 82.8 1.0 O3A A:ADP2001 4.1 82.8 1.0 OD1 A:ASP372 4.1 82.8 1.0 OD2 A:ASP372 4.2 82.8 1.0 CG2 A:THR271 4.2 82.8 1.0 O2B A:ADP2001 4.3 82.8 1.0 F2 A:ALF2002 4.3 82.8 1.0 F3 A:ALF2002 4.4 82.8 1.0 O3B A:ADP2001 4.5 82.8 1.0 CG A:ASP372 4.6 82.8 1.0 CE A:LYS270 4.8 82.8 1.0 O A:GLU702 4.9 82.8 1.0 NZ A:LYS270 4.9 82.8 1.0 CD A:GLU373 4.9 46.6 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Rig-I:Dsrna Filament in Complex with Riplet Pryspry 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 Rig-I:Dsrna Filament in Complex with Riplet Pryspry Domain (Trimer) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2003 b:82.8 occ:1.00 O1B C:ADP2001 2.0 82.8 1.0 F4 C:ALF2002 2.0 82.8 1.0 F1 C:ALF2002 2.1 82.8 1.0 AL C:ALF2002 2.9 82.8 1.0 O1A C:ADP2001 3.4 82.8 1.0 PB C:ADP2001 3.5 82.8 1.0 OE2 C:GLU373 3.7 47.9 1.0 PA C:ADP2001 3.9 82.8 1.0 O2A C:ADP2001 4.0 82.8 1.0 O3A C:ADP2001 4.1 82.8 1.0 OD1 C:ASP372 4.1 82.8 1.0 OD2 C:ASP372 4.2 82.8 1.0 CG2 C:THR271 4.2 82.8 1.0 O2B C:ADP2001 4.3 82.8 1.0 F2 C:ALF2002 4.3 82.8 1.0 F3 C:ALF2002 4.4 82.8 1.0 O3B C:ADP2001 4.5 82.8 1.0 CG C:ASP372 4.6 82.8 1.0 CE C:LYS270 4.8 82.8 1.0 O C:GLU702 4.9 82.8 1.0 NZ C:LYS270 4.9 82.8 1.0 CD C:GLU373 4.9 47.9 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Rig-I:Dsrna Filament in Complex with Riplet Pryspry 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 Rig-I:Dsrna Filament in Complex with Riplet Pryspry Domain (Trimer) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg2003 b:82.8 occ:1.00 O1B E:ADP2001 2.0 82.8 1.0 F4 E:ALF2002 2.0 82.8 1.0 F1 E:ALF2002 2.1 82.8 1.0 AL E:ALF2002 2.9 82.8 1.0 O1A E:ADP2001 3.4 82.8 1.0 PB E:ADP2001 3.5 82.8 1.0 OE2 E:GLU373 3.7 43.6 1.0 PA E:ADP2001 3.9 82.8 1.0 O2A E:ADP2001 4.0 82.8 1.0 O3A E:ADP2001 4.1 82.8 1.0 OD1 E:ASP372 4.1 82.8 1.0 OD2 E:ASP372 4.2 82.8 1.0 CG2 E:THR271 4.2 82.8 1.0 O2B E:ADP2001 4.3 82.8 1.0 F2 E:ALF2002 4.3 82.8 1.0 F3 E:ALF2002 4.4 82.8 1.0 O3B E:ADP2001 4.5 82.8 1.0 CG E:ASP372 4.6 82.8 1.0 CE E:LYS270 4.8 82.8 1.0 O E:GLU702 4.9 82.8 1.0 NZ E:LYS270 4.9 82.8 1.0 CD E:GLU373 4.9 43.6 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