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

The structure of Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form)., PDB code: 5jcf 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 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.920, 132.470, 139.040, 90.00, 90.00, 90.00
R / Rfree (%)	27.7 / 31.2

The structure of Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form). 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 (Orthorhombic Form). (pdb code 5jcf). 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 (Orthorhombic Form)., PDB code: 5jcf:
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 (Orthorhombic Form).


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 (Orthorhombic Form). within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:63.4 occ:1.00 SG A:CYS939 2.3 62.0 1.0 SG A:CYS884 2.3 67.9 1.0 SG A:CYS936 2.3 64.3 1.0 SG A:CYS881 2.3 62.1 1.0 CB A:CYS936 3.3 62.7 1.0 CB A:CYS884 3.4 68.3 1.0 CB A:CYS881 3.4 63.7 1.0 CB A:CYS939 3.4 64.1 1.0 N A:CYS884 3.9 65.6 1.0 CA A:CYS884 4.2 68.3 1.0 N A:CYS939 4.2 65.6 1.0 CA A:CYS939 4.4 64.7 1.0 CB A:GLN941 4.5 57.5 1.0 CB A:ASN883 4.7 62.5 1.0 CA A:CYS936 4.8 63.3 1.0 C A:CYS884 4.8 70.5 1.0 CA A:CYS881 4.8 64.0 1.0 CZ2 A:TRP943 4.9 62.7 1.0 NE1 A:TRP943 4.9 59.6 1.0 C A:ASN883 5.0 65.2 1.0 C A:CYS939 5.0 63.2 1.0 CB A:ASP938 5.0 70.3 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 (Orthorhombic Form).


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 (Orthorhombic Form). within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:65.7 occ:1.00 SG B:CYS884 2.3 70.2 1.0 SG B:CYS939 2.3 64.5 1.0 SG B:CYS936 2.3 66.0 1.0 SG B:CYS881 2.3 64.2 1.0 CB B:CYS936 3.3 64.5 1.0 CB B:CYS884 3.4 71.0 1.0 CB B:CYS881 3.4 65.3 1.0 CB B:CYS939 3.4 66.7 1.0 N B:CYS884 3.9 68.0 1.0 CA B:CYS884 4.2 71.0 1.0 N B:CYS939 4.2 67.7 1.0 CA B:CYS939 4.4 67.2 1.0 CB B:GLN941 4.5 60.4 1.0 CB B:ASN883 4.7 64.7 1.0 CA B:CYS936 4.8 65.1 1.0 C B:CYS884 4.8 73.2 1.0 CA B:CYS881 4.8 65.2 1.0 CZ2 B:TRP943 4.9 64.5 1.0 NE1 B:TRP943 4.9 61.5 1.0 C B:ASN883 5.0 67.5 1.0 CB B:ASP938 5.0 72.1 1.0 C B:CYS939 5.0 65.8 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