Magnesium in PDB 6hdu: Crystal Structure of Human RAB38 in Complex with Gtp

The structure of Crystal Structure of Human RAB38 in Complex with Gtp, PDB code: 6hdu was solved by E.Mcgrath, D.Waschbusch, A.R.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.28 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.045, 70.993, 74.487, 90.00, 102.21, 90.00
R / Rfree (%)	18.8 / 21.2

The binding sites of Magnesium atom in the Crystal Structure of Human RAB38 in Complex with Gtp (pdb code 6hdu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human RAB38 in Complex with Gtp, PDB code: 6hdu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human RAB38 in Complex with Gtp


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 RAB38 in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:15.2 occ:1.00 O3G A:GTP900 2.0 19.9 1.0 O A:HOH1010 2.1 15.1 1.0 OG1 A:THR41 2.1 15.1 1.0 O2B A:GTP900 2.1 12.6 1.0 OG1 A:THR23 2.1 16.0 1.0 O A:HOH1020 2.2 16.7 1.0 CB A:THR41 3.1 20.0 1.0 CB A:THR23 3.2 13.8 1.0 PG A:GTP900 3.2 18.0 1.0 PB A:GTP900 3.3 16.0 1.0 O3B A:GTP900 3.5 17.9 1.0 N A:THR41 3.7 22.1 1.0 N A:THR23 3.9 12.6 1.0 CA A:THR41 4.0 17.1 1.0 O2G A:GTP900 4.1 19.4 1.0 OD2 A:ASP65 4.1 20.6 1.0 OD1 A:ASP65 4.1 18.2 1.0 CA A:THR23 4.1 13.8 1.0 O A:HOH1008 4.1 26.5 1.0 O1A A:GTP900 4.2 13.6 1.0 O1B A:GTP900 4.3 15.4 1.0 CG2 A:THR41 4.3 17.0 1.0 O1G A:GTP900 4.3 16.5 1.0 CG2 A:THR23 4.3 14.6 1.0 O3A A:GTP900 4.4 13.0 1.0 CG A:ASP65 4.5 19.5 1.0 PA A:GTP900 4.6 16.2 1.0 O2A A:GTP900 4.7 13.3 1.0 O A:ARG39 4.8 23.5 1.0 C A:ALA40 4.8 22.0 1.0 CE A:LYS22 4.8 16.4 1.0 CB A:LYS22 4.9 9.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human RAB38 in Complex with Gtp


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 RAB38 in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:18.6 occ:1.00 O3G B:GTP900 2.0 22.1 1.0 O B:HOH1027 2.0 17.2 1.0 O2B B:GTP900 2.1 15.7 1.0 OG1 B:THR23 2.1 16.9 1.0 O B:HOH1030 2.1 20.1 1.0 OG1 B:THR41 2.1 15.7 1.0 CB B:THR23 3.1 14.6 1.0 CB B:THR41 3.2 28.5 1.0 PG B:GTP900 3.2 24.4 1.0 PB B:GTP900 3.3 17.2 1.0 O3B B:GTP900 3.5 18.3 1.0 N B:THR41 3.7 28.5 1.0 N B:THR23 3.9 14.1 1.0 OD2 B:ASP65 4.0 20.7 1.0 CA B:THR41 4.0 22.6 1.0 OD1 B:ASP65 4.1 18.1 1.0 CA B:THR23 4.1 13.1 1.0 O1A B:GTP900 4.1 16.2 1.0 O2G B:GTP900 4.1 25.1 1.0 O1G B:GTP900 4.2 24.8 1.0 CG2 B:THR23 4.2 16.1 1.0 O B:HOH1009 4.2 28.7 1.0 O1B B:GTP900 4.3 17.1 1.0 CG2 B:THR41 4.3 25.3 1.0 O3A B:GTP900 4.4 15.5 1.0 CG B:ASP65 4.4 18.3 1.0 PA B:GTP900 4.6 15.4 1.0 O B:ARG39 4.6 29.8 1.0 O2A B:GTP900 4.7 17.6 1.0 C B:ALA40 4.8 33.9 1.0 CE B:LYS22 4.9 13.6 1.0 CB B:LYS22 4.9 13.4 1.0 C B:LYS22 5.0 17.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human RAB38 in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human RAB38 in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:16.7 occ:1.00 O1G C:GTP900 2.0 19.7 1.0 O C:HOH1021 2.0 15.1 1.0 O1B C:GTP900 2.0 13.4 1.0 OG1 C:THR23 2.0 14.9 1.0 O C:HOH1035 2.1 20.1 1.0 OG1 C:THR41 2.1 16.2 1.0 CB C:THR23 3.1 14.0 1.0 CB C:THR41 3.2 20.1 1.0 PB C:GTP900 3.2 14.8 1.0 PG C:GTP900 3.2 18.6 1.0 O3B C:GTP900 3.5 17.3 1.0 N C:THR41 3.8 19.9 1.0 N C:THR23 3.8 12.7 1.0 OD1 C:ASP65 4.0 21.3 1.0 CA C:THR23 4.1 13.7 1.0 OD2 C:ASP65 4.1 23.4 1.0 O2G C:GTP900 4.1 20.0 1.0 O2A C:GTP900 4.1 16.2 1.0 CA C:THR41 4.1 18.6 1.0 CG2 C:THR23 4.2 19.7 1.0 O2B C:GTP900 4.2 14.0 1.0 CG2 C:THR41 4.3 19.7 1.0 O C:HOH1008 4.3 21.1 1.0 O3G C:GTP900 4.3 18.6 1.0 O3A C:GTP900 4.3 13.8 1.0 CG C:ASP65 4.4 19.9 1.0 PA C:GTP900 4.6 14.9 1.0 O C:ARG39 4.7 22.1 1.0 O1A C:GTP900 4.7 14.4 1.0 CE C:LYS22 4.8 17.9 1.0 CB C:LYS22 4.8 11.7 1.0 C C:ALA40 4.9 28.5 1.0 C C:LYS22 4.9 15.4 1.0 NZ C:LYS22 5.0 16.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human RAB38 in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human RAB38 in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:14.7 occ:1.00 O3G D:GTP900 2.0 16.0 1.0 O2B D:GTP900 2.0 12.7 1.0 OG1 D:THR23 2.1 15.0 1.0 OG1 D:THR41 2.1 15.3 1.0 O D:HOH1015 2.1 16.4 1.0 O D:HOH1028 2.2 16.6 1.0 CB D:THR23 3.1 13.4 1.0 CB D:THR41 3.1 20.3 1.0 PG D:GTP900 3.2 16.9 1.0 PB D:GTP900 3.2 14.9 1.0 O3B D:GTP900 3.6 17.3 1.0 N D:THR41 3.8 19.7 1.0 N D:THR23 3.9 13.7 1.0 OD1 D:ASP65 4.0 19.6 1.0 OD2 D:ASP65 4.1 22.1 1.0 CA D:THR23 4.1 15.8 1.0 CA D:THR41 4.1 15.0 1.0 O2G D:GTP900 4.1 18.0 1.0 O1A D:GTP900 4.1 14.2 1.0 CG2 D:THR23 4.2 15.0 1.0 O D:HOH1012 4.2 24.3 1.0 CG2 D:THR41 4.2 18.2 1.0 O1B D:GTP900 4.2 13.7 1.0 O1G D:GTP900 4.3 18.6 1.0 O3A D:GTP900 4.4 14.4 1.0 CG D:ASP65 4.4 21.1 1.0 PA D:GTP900 4.6 15.5 1.0 O2A D:GTP900 4.7 13.5 1.0 O D:ARG39 4.8 20.9 1.0 CE D:LYS22 4.8 15.7 1.0 C D:ALA40 4.8 25.2 1.0 NH2 D:ARG39 4.9 40.9 1.0 CB D:LYS22 4.9 12.1 1.0

E.Mcgrath, D.Waschbusch, B.M.Baker, A.R.Khan. LRRK2 Binds to the RAB32 Subfamily in A Gtp-Dependent Mannerviaits Armadillo Domain. Small Gtpases 1 2019.
ISSN: ISSN 2154-1256
PubMed: 31552791
DOI: 10.1080/21541248.2019.1666623