Zinc in PDB 5jc3: Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned).

The structure of Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned)., PDB code: 5jc3 was solved by S.Cusack, E.Uchikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.160, 138.700, 100.430, 90.00, 109.47, 90.00
R / Rfree (%)	27.1 / 29

The structure of Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned). also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned). (pdb code 5jc3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned)., PDB code: 5jc3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned). within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:54.5 occ:1.00 SG A:CYS936 2.3 51.2 1.0 SG A:CYS884 2.3 61.5 1.0 SG A:CYS939 2.3 54.3 1.0 SG A:CYS881 2.4 57.0 1.0 CB A:CYS936 3.3 51.7 1.0 CB A:CYS884 3.3 60.2 1.0 CB A:CYS881 3.4 57.3 1.0 CB A:CYS939 3.4 54.4 1.0 N A:CYS884 3.9 56.9 1.0 CA A:CYS884 4.1 60.1 1.0 N A:CYS939 4.2 55.8 1.0 CA A:CYS939 4.4 54.0 1.0 CB A:GLN941 4.5 52.4 1.0 CB A:ASN883 4.7 53.9 1.0 CA A:CYS936 4.8 51.2 1.0 NE1 A:TRP943 4.8 52.3 1.0 C A:CYS884 4.8 61.9 1.0 CA A:CYS881 4.8 57.9 1.0 CZ2 A:TRP943 4.9 54.9 1.0 C A:ASN883 4.9 55.7 1.0 CB A:ASP938 4.9 57.6 1.0 N A:HIS885 5.0 65.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Monoclinic Form, Twinned). within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:56.2 occ:1.00 SG B:CYS939 2.3 54.9 1.0 SG B:CYS884 2.3 62.7 1.0 SG B:CYS936 2.3 55.0 1.0 SG B:CYS881 2.4 60.1 1.0 CB B:CYS936 3.3 53.9 1.0 CB B:CYS884 3.3 62.3 1.0 CB B:CYS881 3.4 60.2 1.0 CB B:CYS939 3.4 55.1 1.0 N B:CYS884 3.9 60.1 1.0 CA B:CYS884 4.1 62.9 1.0 N B:CYS939 4.2 55.0 1.0 CA B:CYS939 4.4 53.9 1.0 CB B:GLN941 4.5 48.8 1.0 CB B:ASN883 4.7 57.2 1.0 CA B:CYS936 4.8 53.4 1.0 NE1 B:TRP943 4.8 52.5 1.0 C B:CYS884 4.8 65.5 1.0 CA B:CYS881 4.8 60.8 1.0 CZ2 B:TRP943 4.9 55.3 1.0 C B:ASN883 4.9 58.8 1.0 CB B:ASP938 5.0 56.2 1.0 N B:HIS885 5.0 68.9 1.0

E.Uchikawa, M.Lethier, H.Malet, J.Brunel, D.Gerlier, S.Cusack. Structural Analysis of Dsrna Binding to Anti-Viral Pattern Recognition Receptors LGP2 and MDA5. Mol.Cell V. 62 586 2016.
ISSN: ISSN 1097-2765
PubMed: 27203181
DOI: 10.1016/J.MOLCEL.2016.04.021