Magnesium in PDB 8jc5: Crystal Structure of PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L)

All present enzymatic activity of Crystal Structure of PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L):
3.6.5.2;

The structure of Crystal Structure of PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L), PDB code: 8jc5 was solved by X.H.Qiu, L.F.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.976, 73.817, 91.959, 90, 114.18, 90
R / Rfree (%)	16.7 / 20.1

The binding sites of Magnesium atom in the Crystal Structure of PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L) (pdb code 8jc5). 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 PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L), PDB code: 8jc5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L)


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 PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:39.4 occ:1.00 O3G A:GTP201 1.9 41.8 1.0 OG1 A:THR34 2.0 46.3 1.0 OG1 A:THR52 2.1 50.5 1.0 O2B A:GTP201 2.2 35.9 1.0 O A:HOH301 2.2 38.3 1.0 O A:HOH310 2.2 44.9 1.0 CB A:THR52 3.1 43.7 1.0 CB A:THR34 3.2 47.2 1.0 PG A:GTP201 3.2 38.3 1.0 PB A:GTP201 3.3 38.0 1.0 O3B A:GTP201 3.6 37.9 1.0 N A:THR52 3.7 43.3 1.0 O1G A:GTP201 3.8 33.2 1.0 N A:THR34 3.9 38.9 1.0 OD1 A:ASP71 3.9 42.1 1.0 OD2 A:ASP71 4.0 42.3 1.0 CA A:THR52 4.0 45.9 1.0 CA A:THR34 4.1 40.6 1.0 O2A A:GTP201 4.2 42.9 1.0 CG2 A:THR34 4.2 44.3 1.0 O1B A:GTP201 4.3 49.1 1.0 CG2 A:THR52 4.4 48.9 1.0 O2G A:GTP201 4.4 38.6 1.0 CG A:ASP71 4.4 48.4 1.0 O3A A:GTP201 4.4 43.5 1.0 PA A:GTP201 4.6 39.2 1.0 O1A A:GTP201 4.7 36.0 1.0 C A:PRO51 4.7 51.4 1.0 O A:ILE50 4.8 50.6 1.0 CB A:LYS33 5.0 34.6 1.0 C A:LYS33 5.0 32.4 1.0 CA A:PRO51 5.0 50.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L)


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 PLEKHM1 Run Domain in Complex with Gtp-Bound ARL8B(Q75L) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:36.4 occ:1.00 O3G B:GTP201 2.0 35.7 1.0 O B:HOH313 2.0 33.9 1.0 OG1 B:THR34 2.1 36.2 1.0 O B:HOH305 2.1 38.0 1.0 OG1 B:THR52 2.2 37.1 1.0 O2B B:GTP201 2.4 26.9 1.0 PG B:GTP201 3.1 36.9 1.0 CB B:THR52 3.2 37.5 1.0 CB B:THR34 3.2 38.1 1.0 O3B B:GTP201 3.5 39.5 1.0 PB B:GTP201 3.6 40.9 1.0 N B:THR52 3.7 35.7 1.0 O1G B:GTP201 3.8 36.9 1.0 N B:THR34 3.9 34.2 1.0 O2A B:GTP201 4.0 40.1 1.0 CA B:THR52 4.0 37.6 1.0 CA B:THR34 4.1 38.8 1.0 OD1 B:ASP71 4.1 38.0 1.0 OD2 B:ASP71 4.2 39.1 1.0 CG2 B:THR34 4.3 38.6 1.0 O B:HOH315 4.3 40.3 1.0 CG2 B:THR52 4.3 40.2 1.0 O2G B:GTP201 4.3 36.3 1.0 O3A B:GTP201 4.3 35.8 1.0 PA B:GTP201 4.5 38.9 1.0 O1A B:GTP201 4.6 33.9 1.0 CG B:ASP71 4.6 42.6 1.0 O B:ILE50 4.7 38.6 1.0 C B:PRO51 4.7 34.7 1.0 ND2 B:ASN56 4.8 48.5 1.0 CB B:LYS33 4.8 36.1 1.0 CA B:PRO51 5.0 36.8 1.0 C B:LYS33 5.0 36.6 1.0

X.Qiu, Y.Li, Y.Wang, X.Gong, Y.Wang, L.Pan. Mechanistic Insights Into the Interactions of ARL8B with the Run Domains of PLEKHM1 and Skip. J.Mol.Biol. V. 435 68293 2023.
ISSN: ESSN 1089-8638
PubMed: 37775038
DOI: 10.1016/J.JMB.2023.168293