Magnesium in PDB 6zay: Crystal Structure of ATG16L in Complex with Gdp-Bound RAB33B

The structure of Crystal Structure of ATG16L in Complex with Gdp-Bound RAB33B, PDB code: 6zay 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)	49.57 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.010, 132.110, 154.370, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.1

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

Magnesium binding site 1 out of 2 in the Crystal Structure of ATG16L in Complex with Gdp-Bound RAB33B


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 Gdp-Bound RAB33B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:56.7 occ:1.00 O1B A:GDP307 2.6 25.5 1.0 OG1 A:THR47 2.7 36.5 1.0 O A:HOH402 2.7 41.8 1.0 OG1 A:THR65 2.7 45.4 1.0 O A:HOH413 2.7 31.2 1.0 O2A A:GDP307 3.1 38.8 1.0 O A:GLU63 3.2 48.1 1.0 O3B A:GDP307 3.2 33.1 1.0 PB A:GDP307 3.4 38.0 1.0 CB A:THR47 3.5 38.4 1.0 N A:THR65 3.6 38.9 1.0 CB A:THR65 3.8 44.1 1.0 PA A:GDP307 4.0 39.3 1.0 O A:HOH401 4.0 49.1 1.0 O3A A:GDP307 4.1 42.9 1.0 C A:GLU63 4.2 51.0 1.0 CA A:THR65 4.3 49.0 1.0 O1A A:GDP307 4.3 30.0 1.0 CG2 A:THR47 4.4 36.5 1.0 C A:ALA64 4.4 44.0 1.0 CA A:ALA64 4.5 48.9 1.0 N A:THR47 4.6 38.9 1.0 CA A:THR47 4.7 39.2 1.0 O2B A:GDP307 4.7 38.4 1.0 OG1 A:THR62 4.7 55.8 1.0 CB A:THR62 4.7 55.8 1.0 N A:ALA64 4.8 43.6 1.0 O A:HOH460 4.8 34.6 1.0 O A:HOH477 4.9 58.5 1.0 OD2 A:ASP88 4.9 52.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of ATG16L in Complex with Gdp-Bound RAB33B


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 Gdp-Bound RAB33B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg310 b:48.3 occ:1.00 O B:HOH404 2.8 42.4 1.0 O B:GLU63 2.8 42.2 1.0 OG1 B:THR65 2.9 55.7 1.0 O2A B:GDP311 2.9 38.0 1.0 OG1 B:THR47 2.9 45.5 1.0 O1B B:GDP311 3.0 30.3 1.0 O B:HOH434 3.2 45.5 1.0 O3B B:GDP311 3.2 32.8 1.0 PB B:GDP311 3.5 39.8 1.0 CB B:THR47 3.6 49.1 1.0 N B:THR65 3.6 47.2 1.0 C B:GLU63 3.8 49.2 1.0 PA B:GDP311 3.9 46.2 1.0 CB B:THR65 4.1 45.0 1.0 O3A B:GDP311 4.1 53.8 1.0 CA B:ALA64 4.2 43.3 1.0 C B:ALA64 4.2 48.0 1.0 O1A B:GDP311 4.3 33.4 1.0 O B:HOH417 4.3 52.1 1.0 CA B:THR65 4.4 51.7 1.0 CG2 B:THR47 4.4 40.2 1.0 N B:ALA64 4.4 48.9 1.0 CB B:THR62 4.4 50.6 1.0 OG1 B:THR62 4.6 49.6 1.0 N B:GLU63 4.7 46.6 1.0 O B:HOH460 4.8 75.2 1.0 CA B:GLU63 4.9 50.1 1.0 O2B B:GDP311 4.9 41.5 1.0 CA B:THR47 4.9 34.9 1.0 N B:THR47 4.9 33.1 1.0 O B:HOH433 5.0 34.1 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