Zinc in PDB 5jc7: Crystal Structure of Chicken MDA5 with 5'P 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution.

The structure of Crystal Structure of Chicken MDA5 with 5'P 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution., PDB code: 5jc7 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 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.750, 133.400, 138.440, 90.00, 90.00, 90.00
R / Rfree (%)	29.1 / 32.2

The structure of Crystal Structure of Chicken MDA5 with 5'P 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution. 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 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution. (pdb code 5jc7). 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 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution., PDB code: 5jc7:
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 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution.


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 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:67.7 occ:1.00 SG A:CYS884 2.3 65.8 1.0 SG A:CYS939 2.3 66.4 1.0 SG A:CYS936 2.3 65.6 1.0 SG A:CYS881 2.4 56.7 1.0 CB A:CYS936 3.2 70.1 1.0 CB A:CYS884 3.3 66.6 1.0 CB A:CYS939 3.3 72.7 1.0 CB A:CYS881 3.3 58.0 1.0 N A:CYS939 3.9 82.4 1.0 N A:CYS884 4.0 66.1 1.0 CA A:CYS939 4.2 77.4 1.0 CA A:CYS884 4.2 66.1 1.0 CB A:ASP938 4.6 86.3 1.0 CB A:GLN941 4.6 88.7 1.0 CA A:CYS936 4.7 74.0 1.0 NE1 A:TRP943 4.7 0.2 1.0 CZ2 A:TRP943 4.7 94.5 1.0 CB A:ASN883 4.8 57.5 1.0 CA A:CYS881 4.8 59.0 1.0 C A:CYS884 4.9 65.4 1.0 C A:ASP938 4.9 85.8 1.0 C A:CYS939 4.9 79.1 1.0 N A:GLY940 5.0 79.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Chicken MDA5 with 5'P 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution.


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 24-Mer Dsrna and Adp-MG2+ at 2.75 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:62.0 occ:1.00 SG B:CYS939 2.3 52.6 1.0 SG B:CYS884 2.3 64.0 1.0 SG B:CYS936 2.3 59.1 1.0 SG B:CYS881 2.4 55.9 1.0 CB B:CYS936 3.2 63.3 1.0 CB B:CYS884 3.3 61.7 1.0 CB B:CYS939 3.3 60.2 1.0 CB B:CYS881 3.4 56.5 1.0 N B:CYS939 3.9 69.4 1.0 N B:CYS884 4.0 57.0 1.0 CA B:CYS939 4.2 64.0 1.0 CA B:CYS884 4.2 59.8 1.0 CB B:ASP938 4.6 75.3 1.0 CB B:GLN941 4.6 75.7 1.0 CA B:CYS936 4.7 66.4 1.0 NE1 B:TRP943 4.7 81.9 1.0 CZ2 B:TRP943 4.8 83.8 1.0 CB B:ASN883 4.8 54.9 1.0 CA B:CYS881 4.8 56.3 1.0 C B:CYS939 4.9 64.8 1.0 C B:ASP938 4.9 74.8 1.0 C B:CYS884 4.9 60.9 1.0 N B:GLY940 5.0 67.8 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