Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1002 b:42.7 occ:1.00 O1B A:ADP1001 1.9 68.8 1.0 O1A A:ADP1001 2.2 71.0 1.0 OG1 A:THR329 2.8 56.8 1.0 PB A:ADP1001 2.9 69.2 1.0 O3A A:ADP1001 2.9 70.1 1.0 PA A:ADP1001 3.1 71.2 1.0 CG2 A:THR329 3.5 53.0 1.0 O3B A:ADP1001 3.6 68.7 1.0 CB A:THR329 3.7 54.0 1.0 N A:THR329 3.9 54.1 1.0 O2B A:ADP1001 4.1 68.7 1.0 O2A A:ADP1001 4.2 70.9 1.0 O5' A:ADP1001 4.3 71.2 1.0 N A:LYS328 4.3 56.8 1.0 CG A:LYS328 4.4 54.2 1.0 CA A:THR329 4.4 53.4 1.0 C5' A:ADP1001 4.5 70.7 1.0 CA A:GLY327 4.6 60.2 1.0 C A:GLY327 4.8 58.1 1.0 OE2 A:GLU369 4.9 64.4 1.0 C A:LYS328 5.0 54.0 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1002 b:41.5 occ:1.00 O3B B:ADP1001 1.9 63.4 1.0 O2A B:ADP1001 2.3 65.9 1.0 OG1 B:THR329 2.9 54.1 1.0 PB B:ADP1001 3.0 63.5 1.0 O3A B:ADP1001 3.0 64.6 1.0 PA B:ADP1001 3.2 65.4 1.0 CG2 B:THR329 3.4 50.1 1.0 CB B:THR329 3.7 51.2 1.0 O2B B:ADP1001 3.8 62.6 1.0 N B:THR329 4.1 51.1 1.0 O1B B:ADP1001 4.2 62.5 1.0 O5' B:ADP1001 4.3 65.5 1.0 O1A B:ADP1001 4.4 65.2 1.0 CG B:LYS328 4.4 51.1 1.0 C5' B:ADP1001 4.4 65.0 1.0 CA B:THR329 4.5 50.6 1.0 N B:LYS328 4.5 53.5 1.0 CA B:GLY327 4.8 56.9 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