Magnesium in PDB 8ij9: Crystal Structure of the ELKS1/RAB6B Complex

All present enzymatic activity of Crystal Structure of the ELKS1/RAB6B Complex:
3.6.5.2;

The structure of Crystal Structure of the ELKS1/RAB6B Complex, PDB code: 8ij9 was solved by G.Jin, Z.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.56 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.193, 93.227, 53.077, 90, 103.74, 90
R / Rfree (%)	17.2 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of the ELKS1/RAB6B Complex (pdb code 8ij9). 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 the ELKS1/RAB6B Complex, PDB code: 8ij9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the ELKS1/RAB6B 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 the ELKS1/RAB6B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:23.4 occ:1.00 O2B A:GTP201 2.0 19.3 1.0 O1G A:GTP201 2.1 24.5 1.0 O A:HOH348 2.1 20.5 1.0 OG1 A:THR27 2.2 21.5 1.0 O A:HOH314 2.3 20.2 1.0 OG1 A:THR45 2.3 22.5 1.0 CB A:THR27 3.2 21.5 1.0 PB A:GTP201 3.2 20.2 1.0 PG A:GTP201 3.3 22.2 1.0 CB A:THR45 3.3 23.4 1.0 O3B A:GTP201 3.5 22.8 1.0 N A:THR45 3.8 23.4 1.0 N A:THR27 3.8 17.2 1.0 O2G A:GTP201 4.1 22.6 1.0 CA A:THR27 4.1 22.4 1.0 OD2 A:ASP68 4.1 23.4 1.0 CA A:THR45 4.1 22.5 1.0 O A:HOH302 4.1 25.6 1.0 OD1 A:ASP68 4.1 25.8 1.0 O2A A:GTP201 4.1 17.8 1.0 O1B A:GTP201 4.2 20.3 1.0 CG2 A:THR27 4.2 20.3 1.0 O3A A:GTP201 4.3 21.2 1.0 O3G A:GTP201 4.3 22.2 1.0 CG2 A:THR45 4.5 22.8 1.0 CG A:ASP68 4.5 22.3 1.0 PA A:GTP201 4.5 22.7 1.0 O A:THR69 4.6 21.4 1.0 O1A A:GTP201 4.7 18.9 1.0 CE A:LYS26 4.7 24.0 1.0 CB A:LYS26 4.8 21.7 1.0 C A:ALA44 4.8 23.1 1.0 O A:GLN43 4.8 21.6 1.0 O A:HOH384 4.9 28.9 1.0 C A:LYS26 4.9 21.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the ELKS1/RAB6B 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 the ELKS1/RAB6B Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:22.4 occ:1.00 O1G B:GTP201 2.0 25.0 1.0 O B:HOH325 2.0 18.9 1.0 O B:HOH322 2.1 22.9 1.0 O2B B:GTP201 2.1 21.4 1.0 OG1 B:THR45 2.1 21.3 1.0 OG1 B:THR27 2.2 20.2 1.0 CB B:THR45 3.1 23.7 1.0 PG B:GTP201 3.2 23.4 1.0 CB B:THR27 3.2 20.9 1.0 PB B:GTP201 3.3 22.4 1.0 O3B B:GTP201 3.5 23.2 1.0 N B:THR45 3.6 25.2 1.0 CA B:THR45 3.9 25.2 1.0 N B:THR27 3.9 17.8 1.0 OD2 B:ASP68 4.0 21.9 1.0 O2G B:GTP201 4.0 26.1 1.0 O2A B:GTP201 4.1 19.5 1.0 CA B:THR27 4.2 20.1 1.0 OD1 B:ASP68 4.2 22.3 1.0 CG2 B:THR45 4.3 23.6 1.0 CG2 B:THR27 4.3 20.6 1.0 O3G B:GTP201 4.3 25.3 1.0 O1B B:GTP201 4.3 19.0 1.0 O B:HOH349 4.4 25.3 1.0 O3A B:GTP201 4.4 24.2 1.0 CG B:ASP68 4.4 23.1 1.0 O B:THR69 4.5 21.4 1.0 C B:ALA44 4.6 25.5 1.0 O B:GLN43 4.6 23.6 1.0 PA B:GTP201 4.6 20.8 1.0 O1A B:GTP201 4.8 21.9 1.0 CB B:LYS26 4.9 19.2 1.0 CE B:LYS26 4.9 20.8 1.0

G.Jin, L.Lin, K.Li, J.Li, C.Yu, Z.Wei. Structural Basis of Elks/RAB6B Interaction and Its Role in Vesicle Capturing Enhanced By Liquid-Liquid Phase Separation. J.Biol.Chem. 04808 2023.
ISSN: ESSN 1083-351X
PubMed: 37172719
DOI: 10.1016/J.JBC.2023.104808