Magnesium in PDB 5jaj: Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.

The structure of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg., PDB code: 5jaj 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)	76.08 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.590, 97.050, 122.520, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 16.8

The structure of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. also contains other interesting chemical elements:

Fluorine	(F)	7 atoms
Aluminium	(Al)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Magnesium atom in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. (pdb code 5jaj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg., PDB code: 5jaj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:18.9 occ:1.00 F1 A:ALF703 2.0 20.8 1.0 O A:HOH922 2.0 20.9 1.0 O3B A:ADP702 2.0 19.2 1.0 O A:HOH851 2.0 17.8 1.0 O A:HOH990 2.1 18.4 1.0 F4 A:ALF703 2.6 25.2 1.0 AL A:ALF703 3.1 17.6 1.0 PB A:ADP702 3.2 18.5 1.0 O2B A:ADP702 3.4 18.1 1.0 O A:HOH1059 3.8 26.5 1.0 OG1 A:THR31 3.8 19.9 1.0 OE2 A:GLU132 3.9 17.8 1.0 O A:HOH836 4.0 16.1 1.0 OD1 A:ASP131 4.0 20.5 1.0 O2A A:ADP702 4.1 22.0 1.0 O3A A:ADP702 4.2 18.7 1.0 CA A:GLY442 4.2 17.8 1.0 OD2 A:ASP131 4.3 19.6 1.0 F3 A:ALF703 4.3 18.0 1.0 O1B A:ADP702 4.3 19.0 1.0 O1A A:ADP702 4.3 20.8 1.0 PA A:ADP702 4.4 19.5 1.0 CE1 A:HIS63 4.4 21.1 1.0 O A:GLY442 4.4 18.3 1.0 CG A:ASP131 4.6 18.4 1.0 F2 A:ALF703 4.7 20.2 1.0 CE A:LYS30 4.8 18.8 1.0 C A:GLY442 4.8 16.6 1.0 NE2 A:HIS63 4.8 21.4 1.0 CD A:GLU132 4.8 16.8 1.0 NH2 A:ARG471 4.9 20.4 1.0 N A:GLY442 5.0 16.5 1.0

Magnesium binding site 2 out of 2 in the Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Chicken LGP2 Witha 5'P 10-Mer Dsrna and Adp-ALF4-Mg. within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg101 b:29.7 occ:1.00 MG Y:MGF101 0.0 29.7 1.0 F2 Y:MGF101 1.7 25.4 1.0 F1 Y:MGF101 1.9 35.7 1.0 F3 Y:MGF101 1.9 48.9 1.0 O X:HOH126 1.9 29.7 1.0 O A:HOH1235 3.6 39.6 1.0 N2 Y:G6 3.7 17.8 1.0 N3 Y:G6 3.7 14.1 1.0 N3 X:G6 3.8 17.4 1.0 O X:HOH136 3.9 32.6 1.0 O A:HOH987 4.0 23.8 1.0 O4' Y:U7 4.0 15.2 1.0 O X:HOH125 4.2 39.9 1.0 C2 Y:G6 4.2 16.3 1.0 O2' Y:G6 4.2 16.1 1.0 C1' Y:U7 4.2 14.8 1.0 NZ A:LYS56 4.2 27.8 0.5 N2 X:G6 4.4 16.6 1.0 C2 X:G6 4.4 16.6 1.0 C1' X:G6 4.5 18.1 1.0 O2' X:G6 4.6 20.8 1.0 C4 X:G6 4.7 16.6 1.0 C2' Y:G6 4.7 13.8 1.0 O2' Y:U7 4.8 15.9 1.0 C1' Y:G6 4.9 14.4 1.0 C4 Y:G6 4.9 15.4 1.0 C2' X:G6 5.0 18.9 1.0 N9 X:G6 5.0 16.6 1.0 N1 Y:U7 5.0 14.3 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