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

Protein crystallography data

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

Magnesium Binding Sites:

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 6q84

Go back to Magnesium Binding Sites List in 6q84
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 6q84

Go back to Magnesium Binding Sites List in 6q84
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

Reference:

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
Page generated: Mon Dec 14 23:51:45 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy