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

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

Zinc 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 Zinc with other atoms in the Zn 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:Zn1101 b:0.6 occ:1.00 SG A:CYS910 2.3 0.5 1.0 SG A:CYS962 2.3 0.3 1.0 SG A:CYS964 2.3 0.5 1.0 SG A:CYS907 2.3 0.8 1.0 CB A:CYS910 2.7 0.5 1.0 N A:CYS910 2.9 0.5 1.0 CB A:CYS907 3.1 0.8 1.0 CA A:CYS910 3.3 0.5 1.0 CB A:CYS964 3.5 0.5 1.0 CB A:CYS962 3.7 0.3 1.0 N A:CYS964 3.9 0.5 1.0 C A:CYS910 4.1 0.5 1.0 C A:ASN909 4.1 0.4 1.0 CB A:ASN909 4.3 0.4 1.0 CA A:CYS964 4.3 0.5 1.0 O A:CYS910 4.4 0.5 1.0 CA A:ASN909 4.6 0.4 1.0 CA A:CYS907 4.6 0.8 1.0 N A:LYS963 4.6 0.5 1.0 N A:ASN909 4.6 0.4 1.0 N A:SER911 4.8 0.9 1.0 CZ2 A:TRP968 4.9 0.3 1.0 OE1 A:GLN966 4.9 0.1 1.0 NE1 A:TRP968 5.0 0.3 1.0 CA A:CYS962 5.0 0.3 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1101 b:0.4 occ:1.00 SG C:CYS910 2.3 0.3 1.0 SG C:CYS962 2.3 0.0 1.0 SG C:CYS964 2.3 0.4 1.0 SG C:CYS907 2.3 0.3 1.0 CB C:CYS910 2.7 0.3 1.0 N C:CYS910 2.9 0.3 1.0 CB C:CYS907 3.1 0.3 1.0 CA C:CYS910 3.3 0.3 1.0 CB C:CYS964 3.5 0.4 1.0 CB C:CYS962 3.7 0.0 1.0 N C:CYS964 3.9 0.4 1.0 C C:CYS910 4.1 0.3 1.0 C C:ASN909 4.1 0.2 1.0 CB C:ASN909 4.3 0.2 1.0 CA C:CYS964 4.3 0.4 1.0 O C:CYS910 4.4 0.3 1.0 CA C:ASN909 4.6 0.2 1.0 CA C:CYS907 4.6 0.3 1.0 N C:LYS963 4.6 0.7 1.0 N C:ASN909 4.6 0.2 1.0 N C:SER911 4.8 0.8 1.0 CZ2 C:TRP968 4.9 1.0 1.0 OE1 C:GLN966 4.9 0.4 1.0 NE1 C:TRP968 5.0 1.0 1.0 CA C:CYS962 5.0 0.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1101 b:0.2 occ:1.00 SG E:CYS910 2.3 0.4 1.0 SG E:CYS962 2.3 0.3 1.0 SG E:CYS964 2.3 0.1 1.0 SG E:CYS907 2.3 0.7 1.0 CB E:CYS910 2.7 0.4 1.0 N E:CYS910 2.9 0.4 1.0 CB E:CYS907 3.1 0.7 1.0 CA E:CYS910 3.3 0.4 1.0 CB E:CYS964 3.5 0.1 1.0 CB E:CYS962 3.7 0.3 1.0 N E:CYS964 3.9 0.1 1.0 C E:CYS910 4.1 0.4 1.0 C E:ASN909 4.1 0.0 1.0 CB E:ASN909 4.3 0.0 1.0 CA E:CYS964 4.3 0.1 1.0 O E:CYS910 4.4 0.4 1.0 CA E:ASN909 4.6 0.0 1.0 CA E:CYS907 4.6 0.7 1.0 N E:LYS963 4.6 0.6 1.0 N E:ASN909 4.6 0.0 1.0 N E:SER911 4.8 0.1 1.0 CZ2 E:TRP968 4.9 0.7 1.0 OE1 E:GLN966 4.9 0.6 1.0 NE1 E:TRP968 5.0 0.7 1.0 CA E:CYS962 5.0 0.3 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