Magnesium in PDB 6wcw: Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7

The structure of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7, PDB code: 6wcw was solved by H.K.Bhargava, J.M.Byck, D.P.Farrell, I.Anishchenko, F.Dimaio, Y.J.Im, J.H.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.22 / 2.80
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.040, 45.330, 186.277, 90.00, 98.51, 90.00
R / Rfree (%)	20 / 25.8

The structure of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 (pdb code 6wcw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7, PDB code: 6wcw:

Magnesium binding site 1 out of 1 in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1402 b:78.0 occ:1.00 OG1 B:THR22 1.8 39.7 1.0 O1G B:GTP1401 1.9 50.9 1.0 OG1 B:THR40 2.0 49.0 1.0 O2B B:GTP1401 2.3 42.0 1.0 CG2 B:THR40 2.8 32.2 1.0 PG B:GTP1401 2.9 50.9 1.0 CB B:THR40 2.9 44.5 1.0 O2G B:GTP1401 3.0 50.1 1.0 CB B:THR22 3.3 32.5 1.0 PB B:GTP1401 3.5 42.1 1.0 OD2 B:ASP63 3.6 50.0 1.0 NZ B:LYS21 3.6 45.5 1.0 O B:THR64 3.6 45.7 1.0 O3B B:GTP1401 3.7 48.3 1.0 N B:THR40 3.7 44.1 1.0 CA B:THR40 3.9 45.3 1.0 N B:THR22 4.0 43.0 1.0 CG2 B:THR22 4.1 24.0 1.0 CA B:THR22 4.2 34.5 1.0 O3G B:GTP1401 4.2 51.4 1.0 O3A B:GTP1401 4.4 45.1 1.0 CG B:ASP63 4.6 49.2 1.0 O1B B:GTP1401 4.6 34.8 1.0 O B:LYS38 4.8 71.0 1.0 C B:THR64 4.9 43.4 1.0 CB B:LYS21 4.9 37.4 1.0 CE B:LYS21 4.9 41.4 1.0 C B:ALA39 4.9 47.9 1.0 C B:THR40 5.0 40.7 1.0

H.K.Bhargava, K.Tabata, J.M.Byck, M.Hamasaki, D.P.Farrell, I.Anishchenko, F.Dimaio, Y.J.Im, T.Yoshimori, J.H.Hurley. Structural Basis For Autophagy Inhibition By the Human Rubicon-RAB7 Complex. Proc.Natl.Acad.Sci.Usa V. 117 17003 2020.
ISSN: ESSN 1091-6490
PubMed: 32632011
DOI: 10.1073/PNAS.2008030117