Magnesium in PDB 3wyf: Crystal Structure of XPO1P-YRB2P-GSP1P-Gtp Complex

The structure of Crystal Structure of XPO1P-YRB2P-GSP1P-Gtp Complex, PDB code: 3wyf was solved by M.Koyama, N.Shirai, Y.Matsuura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.69 / 2.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.490, 155.950, 149.820, 90.00, 106.91, 90.00
R / Rfree (%)	17.5 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of XPO1P-YRB2P-GSP1P-Gtp Complex (pdb code 3wyf). 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 XPO1P-YRB2P-GSP1P-Gtp Complex, PDB code: 3wyf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of XPO1P-YRB2P-GSP1P-Gtp 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 XPO1P-YRB2P-GSP1P-Gtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:24.6 occ:1.00 OG1 A:THR44 1.8 23.8 1.0 O2G A:GTP301 1.9 24.2 1.0 OG1 A:THR26 2.0 24.3 1.0 O2B A:GTP301 2.1 23.6 1.0 O A:HOH477 2.1 21.0 1.0 O A:HOH456 2.2 36.1 1.0 CB A:THR44 3.0 25.3 1.0 CB A:THR26 3.1 24.1 1.0 PG A:GTP301 3.3 26.2 1.0 PB A:GTP301 3.3 22.0 1.0 N A:THR44 3.6 23.8 1.0 O3B A:GTP301 3.6 25.7 1.0 CA A:THR44 3.9 24.1 1.0 N A:THR26 4.0 20.6 1.0 OD1 A:ASP67 4.0 24.9 1.0 CG2 A:THR26 4.1 24.5 1.0 O1G A:GTP301 4.1 21.4 1.0 CA A:THR26 4.1 21.6 1.0 CG2 A:THR44 4.1 23.4 1.0 O A:HOH447 4.2 38.0 1.0 O2A A:GTP301 4.3 27.6 1.0 OD2 A:ASP67 4.3 27.2 1.0 O3A A:GTP301 4.3 28.0 1.0 O1B A:GTP301 4.4 21.7 1.0 O3G A:GTP301 4.4 22.9 1.0 O A:ILE42 4.5 37.0 1.0 CG A:ASP67 4.5 27.3 1.0 O A:THR68 4.6 22.7 1.0 C A:ALA43 4.7 27.2 1.0 PA A:GTP301 4.7 26.0 1.0 O1A A:GTP301 4.8 22.2 1.0 O A:HOH449 4.9 26.0 1.0 CB A:LYS25 4.9 19.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of XPO1P-YRB2P-GSP1P-Gtp 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 XPO1P-YRB2P-GSP1P-Gtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:27.2 occ:1.00 OG1 D:THR26 1.9 24.8 1.0 O2G D:GTP301 2.0 29.0 1.0 O D:HOH486 2.0 21.6 1.0 O1B D:GTP301 2.1 35.0 1.0 O D:HOH462 2.1 32.4 1.0 OG1 D:THR44 2.3 33.5 1.0 CB D:THR26 3.0 28.9 1.0 CB D:THR44 3.2 31.2 1.0 PB D:GTP301 3.3 27.3 1.0 PG D:GTP301 3.3 27.1 1.0 O3B D:GTP301 3.6 33.1 1.0 N D:THR44 3.8 31.4 1.0 N D:THR26 3.9 30.1 1.0 O1A D:GTP301 3.9 27.2 1.0 CG2 D:THR26 4.0 27.9 1.0 O3G D:GTP301 4.0 31.8 1.0 CA D:THR26 4.0 28.4 1.0 OD2 D:ASP67 4.0 30.8 1.0 CA D:THR44 4.1 30.2 1.0 OD1 D:ASP67 4.2 29.2 1.0 O3A D:GTP301 4.3 30.3 1.0 O D:HOH453 4.3 28.8 1.0 O2B D:GTP301 4.4 34.2 1.0 CG2 D:THR44 4.4 27.6 1.0 O1G D:GTP301 4.5 26.0 1.0 PA D:GTP301 4.5 28.1 1.0 CG D:ASP67 4.5 29.3 1.0 O D:ILE42 4.6 33.4 1.0 O D:THR68 4.7 28.7 1.0 O2A D:GTP301 4.8 26.1 1.0 C D:ALA43 4.8 30.3 1.0 O D:HOH455 4.8 29.2 1.0 CB D:LYS25 4.9 28.2 1.0 C D:LYS25 4.9 27.4 1.0

M.Koyama, N.Shirai, Y.Matsuura. Structural Insights Into How YRB2P Accelerates the Assembly of the XPO1P Nuclear Export Complex Cell Rep 2014.
ISSN: ESSN 2211-1247
DOI: 10.1016/J.CELREP.2014.09.052