Magnesium in PDB 6rir: Crystal Structure of Phosphorylated RAB8A in Complex with the Rab- Binding Domain of RILPL2

The structure of Crystal Structure of Phosphorylated RAB8A in Complex with the Rab- Binding Domain of RILPL2, PDB code: 6rir was solved by D.Waschbusch, E.Purlyte, D.R.Alessi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.41 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.333, 71.509, 114.784, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.1

The binding sites of Magnesium atom in the Crystal Structure of Phosphorylated RAB8A in Complex with the Rab- Binding Domain of RILPL2 (pdb code 6rir). 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 Phosphorylated RAB8A in Complex with the Rab- Binding Domain of RILPL2, PDB code: 6rir:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Phosphorylated RAB8A in Complex with the Rab- Binding Domain of RILPL2


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 Phosphorylated RAB8A in Complex with the Rab- Binding Domain of RILPL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:22.9 occ:1.00 O3G A:GTP201 2.0 20.6 1.0 O2B A:GTP201 2.0 20.1 1.0 OG1 A:THR22 2.1 20.4 1.0 OG1 A:THR40 2.1 20.4 1.0 O A:HOH315 2.1 23.4 1.0 O A:HOH356 2.2 24.4 1.0 CB A:THR40 3.1 25.7 1.0 CB A:THR22 3.2 22.6 1.0 PG A:GTP201 3.2 21.9 1.0 PB A:GTP201 3.2 21.4 1.0 O3B A:GTP201 3.5 21.5 1.0 N A:THR40 3.7 23.6 1.0 N A:THR22 3.9 22.0 1.0 O2G A:GTP201 3.9 21.4 1.0 CA A:THR40 4.0 19.7 1.0 OD1 A:ASP63 4.1 25.5 1.0 OD2 A:ASP63 4.1 24.3 1.0 CA A:THR22 4.1 18.0 1.0 O2A A:GTP201 4.2 24.0 1.0 CG2 A:THR22 4.3 21.8 1.0 O1B A:GTP201 4.3 22.8 1.0 CG2 A:THR40 4.3 26.1 1.0 O3A A:GTP201 4.3 23.5 1.0 O A:HOH333 4.3 25.5 1.0 O1G A:GTP201 4.4 21.6 1.0 CG A:ASP63 4.5 26.8 1.0 O A:THR64 4.5 23.1 1.0 PA A:GTP201 4.6 24.2 1.0 O1A A:GTP201 4.6 20.5 1.0 O A:ILE38 4.6 23.5 1.0 C A:SER39 4.7 25.2 1.0 CA A:SER39 4.9 24.9 1.0 CB A:LYS21 5.0 22.5 1.0 C A:LYS21 5.0 24.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Phosphorylated RAB8A in Complex with the Rab- Binding Domain of RILPL2


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 Phosphorylated RAB8A in Complex with the Rab- Binding Domain of RILPL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:26.9 occ:1.00 O3G B:GTP900 2.0 24.1 1.0 O2B B:GTP900 2.1 21.3 1.0 OG1 B:THR40 2.1 28.1 1.0 OG1 B:THR22 2.1 22.8 1.0 O B:HOH1017 2.1 25.2 1.0 O B:HOH1053 2.2 25.0 1.0 CB B:THR40 3.1 27.7 1.0 CB B:THR22 3.2 29.2 1.0 PG B:GTP900 3.2 27.8 1.0 PB B:GTP900 3.2 25.8 1.0 O3B B:GTP900 3.5 29.6 1.0 N B:THR40 3.7 25.6 1.0 OD2 B:ASP63 3.9 33.1 1.0 N B:THR22 3.9 23.1 1.0 O2G B:GTP900 4.0 25.5 1.0 CA B:THR40 4.0 22.9 1.0 CA B:THR22 4.1 23.0 1.0 OD1 B:ASP63 4.2 27.2 1.0 O2A B:GTP900 4.2 31.0 1.0 CG2 B:THR22 4.2 23.2 1.0 CG2 B:THR40 4.3 29.9 1.0 O1B B:GTP900 4.3 25.2 1.0 O B:HOH1027 4.3 31.7 1.0 O3A B:GTP900 4.3 30.3 1.0 O1G B:GTP900 4.3 29.6 1.0 CG B:ASP63 4.4 30.6 1.0 O B:THR64 4.6 23.8 1.0 PA B:GTP900 4.6 28.5 1.0 O B:ILE38 4.6 31.4 1.0 O1A B:GTP900 4.6 26.1 1.0 C B:SER39 4.7 29.8 1.0 CA B:SER39 5.0 30.9 1.0

D.Waschbusch, E.Purlyte, P.Pal, E.Mcgrath, D.R.Alessi, A.R.Khan. Structural Basis For RAB8A Gtpase Recruitment of RILPL2 Via LRRK2-Mediated Phosphorylation of Switch 2 Structure 2020.
ISSN: ISSN 0969-2126
DOI: 10.2139/SSRN.3451451