Magnesium in PDB 5h1y: Crystal Structure of the DDX41 Dead Domain in Complex with SO42- and MG2+

All present enzymatic activity of Crystal Structure of the DDX41 Dead Domain in Complex with SO42- and MG2+:
3.6.4.13;

The structure of Crystal Structure of the DDX41 Dead Domain in Complex with SO42- and MG2+, PDB code: 5h1y was solved by Y.Jiang, S.Ouyang, Z.J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.89 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.881, 62.746, 92.881, 90.00, 94.32, 90.00
R / Rfree (%)	18.6 / 23.3

The binding sites of Magnesium atom in the Crystal Structure of the DDX41 Dead Domain in Complex with SO42- and MG2+ (pdb code 5h1y). 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 the DDX41 Dead Domain in Complex with SO42- and MG2+, PDB code: 5h1y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the DDX41 Dead Domain in Complex with SO42- and MG2+


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 the DDX41 Dead Domain in Complex with SO42- and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:43.5 occ:1.00 OE2 A:GLU345 2.4 30.5 1.0 OG1 A:THR227 2.6 37.5 1.0 NZ A:LYS231 2.7 30.1 1.0 O A:HOH624 2.8 27.0 1.0 CE A:LYS231 3.2 32.7 1.0 CD A:GLU345 3.3 29.9 1.0 CG A:GLU345 3.5 26.5 1.0 CB A:THR227 3.6 33.3 1.0 CG2 A:THR227 3.7 31.1 1.0 CA A:THR227 4.0 29.2 1.0 O A:HOH606 4.1 30.2 1.0 N A:THR227 4.5 28.6 1.0 OE1 A:GLU345 4.5 32.4 1.0 OD1 A:ASP344 4.6 24.8 1.0 O A:HOH655 4.7 36.6 1.0 CD1 A:LEU269 4.7 26.9 1.0 CD A:LYS231 4.7 30.4 1.0 O4 A:SO4501 4.8 29.8 1.0 OD2 A:ASP344 4.8 25.3 1.0 CD2 A:LEU269 4.8 29.6 1.0 O A:HOH636 4.9 26.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the DDX41 Dead Domain in Complex with SO42- and MG2+


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 the DDX41 Dead Domain in Complex with SO42- and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.1 occ:1.00 OE2 B:GLU345 2.6 26.2 1.0 OG1 B:THR227 2.7 39.0 1.0 NZ B:LYS231 2.7 28.5 1.0 O B:HOH661 2.8 29.8 1.0 CE B:LYS231 3.2 27.5 1.0 CD B:GLU345 3.4 28.9 1.0 CG B:GLU345 3.4 22.8 1.0 CB B:THR227 3.5 28.5 1.0 CG2 B:THR227 3.6 27.7 1.0 CA B:THR227 3.8 31.0 1.0 O B:HOH616 4.1 28.3 1.0 N B:THR227 4.3 29.6 1.0 O3 B:SO4501 4.4 34.1 1.0 CD2 B:LEU269 4.6 27.9 1.0 OE1 B:GLU345 4.6 27.5 1.0 CD B:LYS231 4.7 26.6 1.0 OD1 B:ASP344 4.7 24.5 1.0 O B:HOH653 4.7 22.7 1.0 O B:HOH670 4.7 30.7 1.0 OD2 B:ASP344 4.8 26.5 1.0 CD1 B:LEU269 4.9 28.2 1.0 CB B:GLU345 5.0 19.5 1.0

Y.Jiang, Y.Zhu, W.Qiu, Y.J.Liu, G.Cheng, Z.J.Liu, S.Ouyang. Structural and Functional Analyses of Human DDX41 Dead Domain Protein Cell V. 8 72 2017.
ISSN: ESSN 1674-8018
PubMed: 27928732
DOI: 10.1007/S13238-016-0351-9