Magnesium in PDB 5dlq: Crystal Structure of Rangtp-Exportin 4-EIF5A Complex

The structure of Crystal Structure of Rangtp-Exportin 4-EIF5A Complex, PDB code: 5dlq was solved by M.Aksu, S.Trakhanov, D.Gorlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.41 / 3.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.616, 98.616, 726.864, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 27

The binding sites of Magnesium atom in the Crystal Structure of Rangtp-Exportin 4-EIF5A Complex (pdb code 5dlq). 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 Rangtp-Exportin 4-EIF5A Complex, PDB code: 5dlq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Rangtp-Exportin 4-EIF5A 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 Rangtp-Exportin 4-EIF5A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg218 b:58.6 occ:1.00 OG1 C:THR42 2.2 80.3 1.0 O2B C:GTP217 2.3 59.8 1.0 OG1 C:THR24 2.3 75.0 1.0 O3G C:GTP217 2.4 61.2 1.0 CB C:THR42 3.1 72.5 1.0 PG C:GTP217 3.2 61.0 1.0 PB C:GTP217 3.3 62.2 1.0 O1G C:GTP217 3.3 59.9 1.0 NZ C:LYS23 3.3 76.2 1.0 OD1 C:ASP65 3.3 75.0 1.0 O3B C:GTP217 3.5 60.6 1.0 O1B C:GTP217 3.6 58.4 1.0 O C:THR66 3.6 69.8 1.0 CB C:THR24 3.7 73.3 1.0 OD2 C:ASP65 3.8 87.9 1.0 N C:THR24 3.9 70.1 1.0 CG C:ASP65 3.9 77.3 1.0 CG2 C:THR42 4.1 70.2 1.0 N C:THR42 4.1 77.0 1.0 CA C:THR42 4.2 72.5 1.0 CB C:LYS23 4.4 69.6 1.0 CA C:THR24 4.4 74.9 1.0 C C:THR66 4.6 71.6 1.0 CG2 C:THR24 4.7 80.1 1.0 O3A C:GTP217 4.7 61.2 1.0 CE C:LYS23 4.7 72.0 1.0 O2G C:GTP217 4.7 63.1 1.0 CA C:ALA67 4.9 70.8 1.0 C C:LYS23 4.9 71.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Rangtp-Exportin 4-EIF5A 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 Rangtp-Exportin 4-EIF5A Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg218 b:82.0 occ:1.00 O1B D:GTP217 2.1 81.7 1.0 OG1 D:THR42 2.1 99.5 1.0 OG1 D:THR24 2.2 81.8 1.0 O1G D:GTP217 2.2 93.4 1.0 CB D:THR42 3.0 94.5 1.0 PG D:GTP217 3.0 85.2 1.0 O2G D:GTP217 3.1 84.6 1.0 PB D:GTP217 3.3 85.6 1.0 O3B D:GTP217 3.4 84.1 1.0 NZ D:LYS23 3.5 90.1 1.0 CB D:THR24 3.6 81.3 1.0 OD1 D:ASP65 3.7 88.1 1.0 N D:THR42 3.9 87.8 1.0 N D:THR24 3.9 94.2 1.0 OD2 D:ASP65 3.9 99.3 1.0 O D:THR66 4.0 99.5 1.0 CA D:THR42 4.0 89.1 1.0 CG2 D:THR42 4.0 89.5 1.0 CG D:ASP65 4.2 94.0 1.0 O2B D:GTP217 4.2 81.4 1.0 CA D:THR24 4.3 91.5 1.0 CB D:LYS23 4.5 82.5 1.0 O3A D:GTP217 4.5 83.5 1.0 O3G D:GTP217 4.5 87.9 1.0 CG2 D:THR24 4.5 91.1 1.0 O1A D:GTP217 4.6 84.4 1.0 CE D:LYS23 4.9 86.3 1.0 C D:LYS23 4.9 89.1 1.0 C D:THR66 5.0 92.7 1.0

M.Aksu, S.Trakhanov, D.Gorlich. Structure of the Exportin XPO4 in Complex with Rangtp and the Hypusine-Containing Translation Factor EIF5A. Nat Commun V. 7 11952 2016.
ISSN: ESSN 2041-1723
PubMed: 27306458
DOI: 10.1038/NCOMMS11952