Magnesium in PDB 6y09: Crystal Structure of ATG16L in Complex with Gtp-Bound RAB33B (Q92L)

The structure of Crystal Structure of ATG16L in Complex with Gtp-Bound RAB33B (Q92L), PDB code: 6y09 was solved by S.Pantoom, Y.W.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.17 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.950, 132.420, 155.130, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.1

The binding sites of Magnesium atom in the Crystal Structure of ATG16L in Complex with Gtp-Bound RAB33B (Q92L) (pdb code 6y09). 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 ATG16L in Complex with Gtp-Bound RAB33B (Q92L), PDB code: 6y09:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of ATG16L in Complex with Gtp-Bound RAB33B (Q92L)


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 ATG16L in Complex with Gtp-Bound RAB33B (Q92L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:41.2 occ:1.00 O2G A:GTP302 2.0 30.9 1.0 O A:HOH415 2.0 33.5 1.0 OG1 A:THR47 2.0 35.9 1.0 OG1 A:THR65 2.1 46.8 1.0 O2B A:GTP302 2.2 27.9 1.0 O A:HOH417 2.2 41.5 1.0 CB A:THR65 3.1 41.7 1.0 PG A:GTP302 3.2 39.1 1.0 CB A:THR47 3.2 36.0 1.0 PB A:GTP302 3.4 33.5 1.0 O3B A:GTP302 3.6 39.3 1.0 N A:THR65 3.7 35.9 1.0 OD2 A:ASP88 3.9 52.1 1.0 O1G A:GTP302 3.9 37.7 1.0 N A:THR47 3.9 30.6 1.0 CA A:THR65 3.9 43.1 1.0 OD1 A:ASP88 4.0 48.9 1.0 CA A:THR47 4.1 30.5 1.0 O2A A:GTP302 4.2 37.8 1.0 CG2 A:THR65 4.2 40.6 1.0 O A:HOH403 4.3 37.7 1.0 CG2 A:THR47 4.3 31.3 1.0 O1B A:GTP302 4.4 40.0 1.0 O3G A:GTP302 4.4 37.0 1.0 CG A:ASP88 4.4 42.3 1.0 O3A A:GTP302 4.5 58.6 1.0 O A:GLU63 4.5 39.5 1.0 O A:THR89 4.6 35.7 1.0 PA A:GTP302 4.6 38.0 1.0 O1A A:GTP302 4.8 40.1 1.0 C A:ALA64 4.8 39.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of ATG16L in Complex with Gtp-Bound RAB33B (Q92L)


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 ATG16L in Complex with Gtp-Bound RAB33B (Q92L) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:53.7 occ:1.00 OG1 B:THR47 1.9 37.6 1.0 O1G B:GTP302 2.0 41.6 1.0 OG1 B:THR65 2.1 51.9 1.0 O1B B:GTP302 2.2 30.2 1.0 CB B:THR47 3.1 39.4 1.0 CB B:THR65 3.2 32.4 1.0 PG B:GTP302 3.3 39.1 1.0 PB B:GTP302 3.4 34.7 1.0 O3B B:GTP302 3.7 35.4 1.0 N B:THR65 3.7 36.4 1.0 N B:THR47 3.8 29.9 1.0 OD2 B:ASP88 3.8 44.5 1.0 OD1 B:ASP88 3.9 41.2 1.0 O2G B:GTP302 4.0 43.1 1.0 CA B:THR47 4.0 30.1 1.0 CA B:THR65 4.0 46.2 1.0 CG2 B:THR47 4.2 36.9 1.0 CG B:ASP88 4.3 46.5 1.0 O B:GLU63 4.3 39.7 1.0 O B:HOH404 4.3 49.2 1.0 CG2 B:THR65 4.3 32.1 1.0 O3A B:GTP302 4.3 39.6 1.0 O2A B:GTP302 4.3 38.8 1.0 O3G B:GTP302 4.4 35.5 1.0 O2B B:GTP302 4.5 43.6 1.0 O1A B:GTP302 4.5 30.7 1.0 PA B:GTP302 4.6 38.9 1.0 O B:THR89 4.6 45.0 1.0 C B:ALA64 4.8 39.5 1.0 CB B:LYS46 4.9 25.6 1.0 C B:LYS46 4.9 33.9 1.0

S.Pantoom, G.Konstantinidis, S.Voss, H.Han, O.Hofnagel, Z.Li, Y.W.Wu. RAB33B Recruits the ATG16L1 Complex to the Phagophore Via A Noncanonical Rab Binding Protein. Autophagy 1 2020.
ISSN: ESSN 1554-8635
PubMed: 32960676
DOI: 10.1080/15548627.2020.1822629