Zinc 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
Magnesium	(Mg)	3 atoms
Aluminium	(Al)	3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of Rig-I:Dsrna Filament in Complex with Riplet Pryspry Domain (Trimer), PDB code: 7jl3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc 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 Zinc with other atoms in the Zn 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:Zn2004 b:0.9 occ:1.00 SG A:CYS813 2.3 0.1 1.0 SG A:CYS864 2.3 1.0 1.0 SG A:CYS869 2.3 0.2 1.0 SG A:CYS810 2.3 0.7 1.0 CB A:CYS869 3.0 0.2 1.0 CB A:CYS813 3.2 0.1 1.0 CB A:CYS810 3.2 0.7 1.0 CB A:CYS864 3.3 1.0 1.0 N A:CYS813 3.7 0.1 1.0 CA A:CYS813 4.0 0.1 1.0 CB A:HIS871 4.4 0.6 1.0 CA A:CYS869 4.4 0.2 1.0 NE1 A:TRP873 4.6 0.1 1.0 CA A:CYS810 4.7 0.7 1.0 C A:LYS812 4.7 0.8 1.0 CA A:CYS864 4.7 1.0 1.0 O A:CYS869 4.7 0.2 1.0 C A:CYS813 4.7 0.1 1.0 CB A:LYS812 4.8 0.8 1.0 C A:CYS869 4.8 0.2 1.0 CZ2 A:TRP873 4.8 0.1 1.0 N A:LYS812 4.9 0.8 1.0 CB A:ALA815 5.0 0.7 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn2004 b:0.8 occ:1.00 SG C:CYS813 2.3 0.2 1.0 SG C:CYS864 2.3 0.9 1.0 SG C:CYS869 2.3 0.9 1.0 SG C:CYS810 2.3 0.8 1.0 CB C:CYS869 3.0 0.9 1.0 CB C:CYS813 3.2 0.2 1.0 CB C:CYS810 3.2 0.8 1.0 CB C:CYS864 3.3 0.9 1.0 N C:CYS813 3.7 0.2 1.0 CA C:CYS813 4.0 0.2 1.0 CB C:HIS871 4.4 0.6 1.0 CA C:CYS869 4.4 0.9 1.0 NE1 C:TRP873 4.6 0.0 1.0 CA C:CYS810 4.7 0.8 1.0 C C:LYS812 4.7 0.4 1.0 CA C:CYS864 4.7 0.9 1.0 O C:CYS869 4.7 0.9 1.0 C C:CYS813 4.7 0.2 1.0 CB C:LYS812 4.8 0.4 1.0 C C:CYS869 4.8 0.9 1.0 CZ2 C:TRP873 4.8 0.0 1.0 N C:LYS812 4.9 0.4 1.0 CB C:ALA815 5.0 0.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn2004 b:0.4 occ:1.00 SG E:CYS813 2.3 0.3 1.0 SG E:CYS864 2.3 0.2 1.0 SG E:CYS869 2.3 1.0 1.0 SG E:CYS810 2.3 0.5 1.0 CB E:CYS869 3.0 1.0 1.0 CB E:CYS813 3.2 0.3 1.0 CB E:CYS810 3.2 0.5 1.0 CB E:CYS864 3.3 0.2 1.0 N E:CYS813 3.7 0.3 1.0 CA E:CYS813 4.0 0.3 1.0 CB E:HIS871 4.4 0.2 1.0 CA E:CYS869 4.4 1.0 1.0 NE1 E:TRP873 4.6 0.9 1.0 CA E:CYS810 4.7 0.5 1.0 C E:LYS812 4.7 0.5 1.0 CA E:CYS864 4.7 0.2 1.0 O E:CYS869 4.7 1.0 1.0 C E:CYS813 4.7 0.3 1.0 CB E:LYS812 4.8 0.5 1.0 C E:CYS869 4.8 1.0 1.0 CZ2 E:TRP873 4.8 0.9 1.0 N E:LYS812 4.9 0.5 1.0 CB E:ALA815 5.0 0.2 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