Magnesium in PDB 5yu6: Crystal Structure of Exportin-5:Rangtp Complex

The structure of Crystal Structure of Exportin-5:Rangtp Complex, PDB code: 5yu6 was solved by R.Yamazawa, C.Jiko, S.J.Lee, E.Yamashita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.98 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.560, 302.678, 88.264, 90.00, 109.24, 90.00
R / Rfree (%)	21.8 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of Exportin-5:Rangtp Complex (pdb code 5yu6). 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 Exportin-5:Rangtp Complex, PDB code: 5yu6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Exportin-5:Rangtp Complex


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 Exportin-5:Rangtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:41.8 occ:1.00 CG2 B:THR24 2.3 72.6 1.0 O1G B:GTP301 2.5 48.0 1.0 OG1 B:THR42 2.7 37.3 1.0 O B:THR66 3.1 46.9 1.0 O2B B:GTP301 3.1 50.3 1.0 CB B:THR42 3.2 40.4 1.0 O2G B:GTP301 3.3 42.2 1.0 OD1 B:ASP65 3.3 52.8 1.0 PG B:GTP301 3.4 49.8 1.0 OD2 B:ASP65 3.5 52.9 1.0 CG B:ASP65 3.7 48.4 1.0 CB B:THR24 3.8 78.2 1.0 C B:THR66 3.9 45.0 1.0 CG2 B:THR42 4.0 45.3 1.0 O3B B:GTP301 4.0 46.1 1.0 PB B:GTP301 4.2 42.0 1.0 N B:THR24 4.2 65.5 1.0 CG B:LYS23 4.3 32.8 1.0 CA B:ALA67 4.3 58.2 1.0 CE B:LYS23 4.3 29.4 1.0 N B:THR42 4.4 48.3 1.0 CA B:THR42 4.4 48.0 1.0 N B:ALA67 4.4 53.5 1.0 CA B:THR24 4.5 69.0 1.0 OG1 B:THR24 4.5 94.1 1.0 O B:ASP65 4.6 43.2 1.0 NZ B:LYS23 4.6 33.0 1.0 O3G B:GTP301 4.7 48.3 1.0 C B:ASP65 4.7 43.4 1.0 N B:THR66 4.7 48.2 1.0 CD B:LYS23 4.8 29.9 1.0 N B:GLY68 4.9 73.9 1.0 CA B:THR66 5.0 45.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Exportin-5:Rangtp Complex


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 Exportin-5:Rangtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:55.0 occ:1.00 OG1 D:THR24 1.9 62.3 1.0 O3G D:GTP301 2.0 56.9 1.0 OG1 D:THR42 2.2 57.0 1.0 O2B D:GTP301 2.4 66.4 1.0 PG D:GTP301 3.1 49.3 1.0 CB D:THR24 3.1 62.6 1.0 O2A D:GTP301 3.1 56.2 1.0 O3B D:GTP301 3.2 52.3 1.0 PB D:GTP301 3.3 56.8 1.0 CB D:THR42 3.5 55.5 1.0 N D:THR24 3.6 52.2 1.0 OD2 D:ASP65 3.8 45.2 1.0 O2G D:GTP301 3.9 62.4 1.0 CA D:THR24 4.0 61.0 1.0 PA D:GTP301 4.0 46.3 1.0 N D:THR42 4.0 68.3 1.0 OD1 D:ASP65 4.1 53.4 1.0 O3A D:GTP301 4.1 53.1 1.0 O1G D:GTP301 4.2 40.0 1.0 CG2 D:THR24 4.2 61.4 1.0 CG D:ASP65 4.3 47.4 1.0 O1A D:GTP301 4.3 56.7 1.0 CA D:THR42 4.3 61.9 1.0 CG2 D:THR42 4.5 55.6 1.0 O D:VAL40 4.5 56.5 1.0 CB D:LYS23 4.6 48.5 1.0 O1B D:GTP301 4.6 54.3 1.0 C D:LYS23 4.7 48.3 1.0 O D:THR66 4.9 55.5 1.0 N D:LYS23 5.0 39.4 1.0 CA D:LYS23 5.0 41.7 1.0

R.Yamazawa, C.Jiko, S.Choi, I.Y.Park, A.Nakagawa, E.Yamashita, S.J.Lee. Structural Basis For Selective Binding of Export Cargoes By Exportin-5 Structure V. 26 1393 2018.
ISSN: ISSN 1878-4186
PubMed: 30100359
DOI: 10.1016/J.STR.2018.06.014