Magnesium in PDB 6q84: Crystal Structure of Rangtp-PDR6-EIF5A Export Complex

The structure of Crystal Structure of Rangtp-PDR6-EIF5A Export Complex, PDB code: 6q84 was solved by M.Aksu, S.Trakhanov, A.Vera-Rodriguez, D.Gorlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 3.70
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	139.540, 139.540, 346.570, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of Rangtp-PDR6-EIF5A Export Complex (pdb code 6q84). 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-PDR6-EIF5A Export Complex, PDB code: 6q84:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Rangtp-PDR6-EIF5A Export 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-PDR6-EIF5A Export Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg218 b:0.9 occ:1.00 O2B B:GTP217 2.1 0.8 1.0 OG1 B:THR24 2.1 0.4 1.0 O3G B:GTP217 2.1 0.7 1.0 OG1 B:THR42 2.3 0.1 1.0 O1G B:GTP217 2.4 0.5 1.0 PG B:GTP217 2.7 0.9 1.0 CB B:THR42 3.2 0.5 1.0 PB B:GTP217 3.2 0.3 1.0 OD2 B:ASP65 3.3 0.1 1.0 O3B B:GTP217 3.4 0.5 1.0 CB B:THR24 3.4 0.3 1.0 N B:THR24 3.6 0.6 1.0 OD1 B:ASP65 3.6 0.7 1.0 CG B:ASP65 3.9 0.8 1.0 O2A B:GTP217 3.9 0.4 1.0 CA B:THR24 4.0 0.1 1.0 N B:THR42 4.0 0.9 1.0 O2G B:GTP217 4.0 0.5 1.0 O B:THR66 4.2 0.8 1.0 CA B:THR42 4.2 0.1 1.0 CB B:LYS23 4.2 0.4 1.0 CG2 B:THR42 4.3 0.7 1.0 O3A B:GTP217 4.3 0.8 1.0 O1B B:GTP217 4.3 0.8 1.0 CE B:LYS23 4.3 0.4 1.0 PA B:GTP217 4.4 0.2 1.0 NZ B:LYS23 4.5 0.1 1.0 O1A B:GTP217 4.5 0.3 1.0 CG2 B:THR24 4.5 0.0 1.0 C B:LYS23 4.5 0.6 1.0 O B:VAL40 4.8 0.4 1.0 CA B:LYS23 4.8 0.3 1.0 N B:LYS23 4.9 0.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Rangtp-PDR6-EIF5A Export 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-PDR6-EIF5A Export Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg218 b:0.1 occ:1.00 OG1 E:THR42 2.1 0.8 1.0 OG1 E:THR24 2.1 0.8 1.0 O1B E:GTP217 2.2 0.2 1.0 O2G E:GTP217 2.5 0.1 1.0 OD2 E:ASP65 2.9 0.2 1.0 CB E:THR42 2.9 0.3 1.0 O3G E:GTP217 3.0 0.5 1.0 OD1 E:ASP65 3.1 0.8 1.0 PG E:GTP217 3.2 0.1 1.0 CG E:ASP65 3.4 0.6 1.0 PB E:GTP217 3.5 0.1 1.0 O E:THR66 3.5 0.3 1.0 CB E:THR24 3.5 0.6 1.0 N E:THR24 3.7 0.3 1.0 O3B E:GTP217 3.7 0.6 1.0 CG2 E:THR42 3.8 0.3 1.0 CA E:THR24 4.1 0.4 1.0 CA E:THR42 4.2 0.8 1.0 N E:THR42 4.2 0.6 1.0 CB E:LYS23 4.2 0.5 1.0 O1A E:GTP217 4.2 0.5 1.0 CE E:LYS23 4.3 0.0 1.0 O2B E:GTP217 4.4 0.5 1.0 CG2 E:THR24 4.5 0.5 1.0 O1G E:GTP217 4.5 0.5 1.0 O3A E:GTP217 4.6 0.6 1.0 C E:LYS23 4.6 0.5 1.0 O2A E:GTP217 4.6 0.5 1.0 C E:THR66 4.6 0.9 1.0 NZ E:LYS23 4.6 0.1 1.0 PA E:GTP217 4.7 0.6 1.0 CB E:ASP65 4.8 0.1 1.0 CA E:LYS23 4.9 0.8 1.0

M.Aksu, S.Trakhanov, A.Vera Rodriguez, D.Gorlich. Structural Basis For the Nuclear Import and Export Functions of the Biportin PDR6/KAP122. J.Cell Biol. V. 218 1839 2019.
ISSN: ESSN 1540-8140
PubMed: 31023722
DOI: 10.1083/JCB.201812093