Magnesium in PDB 9ltp: Crystal Structure of Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain

The structure of Crystal Structure of Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain, PDB code: 9ltp was solved by J.Wang, W.P.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.99 / 2.49
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.669, 65.483, 98.76, 89.4, 76.73, 67.36
R / Rfree (%)	23.9 / 29.8

The structure of Crystal Structure of Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain also contains other interesting chemical elements:

Aluminium	(Al)	2 atoms
Fluorine	(F)	6 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain (pdb code 9ltp). 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 Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain, PDB code: 9ltp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain


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 Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:12.2 occ:1.00 OG1 B:THR50 2.1 12.0 1.0 F1 B:AF3203 2.2 30.3 1.0 O2B B:GDP202 2.2 22.7 1.0 OG1 B:THR32 2.4 13.7 1.0 CB B:THR50 2.8 15.6 1.0 O B:HOH307 2.9 12.3 1.0 O3B B:GDP202 3.3 28.6 1.0 PB B:GDP202 3.3 13.6 1.0 OD2 B:ASP73 3.4 17.9 1.0 AL B:AF3203 3.4 47.6 1.0 O B:THR74 3.6 16.6 1.0 OD1 B:ASP73 3.6 26.0 1.0 CB B:THR32 3.7 16.2 1.0 CG2 B:THR50 3.8 18.6 1.0 F3 B:AF3203 3.8 26.0 1.0 CG B:ASP73 3.8 29.5 1.0 N B:THR50 3.9 23.0 1.0 CA B:THR50 3.9 22.6 1.0 N B:THR32 4.1 20.9 1.0 O1B B:GDP202 4.2 16.7 1.0 CA B:THR32 4.4 24.8 1.0 O3A B:GDP202 4.5 18.0 1.0 O2A B:GDP202 4.6 17.7 1.0 CE B:LYS31 4.7 16.0 1.0 C B:THR74 4.7 24.2 1.0 CB B:LYS31 4.7 16.4 1.0 CG2 B:THR32 4.7 12.9 1.0 F2 B:AF3203 4.9 20.9 1.0 NZ B:LYS31 4.9 13.8 1.0 C B:SER49 4.9 11.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain


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 Human RAB43 in Gdp-ALF3 Transition State Complex with USP6NL Tbc Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:16.2 occ:1.00 OG1 D:THR32 2.0 19.5 1.0 F3 D:AF3203 2.0 29.1 1.0 O1B D:GDP202 2.1 12.6 1.0 OG1 D:THR50 2.2 33.8 1.0 O D:HOH302 2.3 20.8 1.0 CB D:THR50 3.0 20.4 1.0 PB D:GDP202 3.2 25.1 1.0 CB D:THR32 3.3 19.4 1.0 O2B D:GDP202 3.4 19.8 1.0 N D:THR50 3.4 11.5 1.0 AL D:AF3203 3.5 33.8 1.0 O2A D:GDP202 3.6 12.4 1.0 OD2 D:ASP73 3.7 26.8 1.0 CA D:THR50 3.8 20.6 1.0 O3A D:GDP202 3.9 19.3 1.0 N D:THR32 4.0 22.1 1.0 PA D:GDP202 4.1 23.2 1.0 F2 D:AF3203 4.2 33.9 1.0 O1A D:GDP202 4.2 13.1 1.0 CA D:THR32 4.2 17.1 1.0 CG2 D:THR32 4.3 12.3 1.0 CG2 D:THR50 4.3 15.3 1.0 NH1 C:ARG150 4.4 13.2 1.0 O D:THR74 4.4 17.1 1.0 O3B D:GDP202 4.4 16.9 1.0 C D:SER49 4.6 11.4 1.0 O D:GLY48 4.6 14.3 1.0 CG D:ASP73 4.6 23.4 1.0 OD1 D:ASP73 4.7 23.0 1.0 F1 D:AF3203 4.8 25.5 1.0 CA D:SER49 4.8 21.2 1.0 NZ D:LYS31 5.0 12.8 1.0 C D:THR50 5.0 12.2 1.0

J.Wang, T.Liu, Z.Zhang, W.Yan. Molecular Basis of RAB43 Inactivation By Rn-Tre in Endocytic Trafficking Unveils A General Rab-Gap Recognition Mechanism. Int.J.Biol.Macromol. V. 338 49561 2025.
ISSN: ISSN 0141-8130
PubMed: 41401861
DOI: 10.1016/J.IJBIOMAC.2025.149561