Magnesium in PDB 6sur: The RAB33B-ATG16L1 Crystal Structure

The structure of The RAB33B-ATG16L1 Crystal Structure, PDB code: 6sur was solved by J.Metje-Sprink, K.Kuehnel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 3.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.400, 204.900, 107.200, 90.00, 92.60, 90.00
R / Rfree (%)	20.6 / 23.9

The binding sites of Magnesium atom in the The RAB33B-ATG16L1 Crystal Structure (pdb code 6sur). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The RAB33B-ATG16L1 Crystal Structure, PDB code: 6sur:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the The RAB33B-ATG16L1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The RAB33B-ATG16L1 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:32.7 occ:1.00 O2B A:GTP301 1.9 44.8 1.0 OG1 A:THR65 2.0 39.0 1.0 OG1 A:THR47 2.0 34.4 1.0 O1G A:GTP301 2.3 38.1 1.0 CB A:THR65 2.9 33.0 1.0 PB A:GTP301 3.2 40.6 1.0 OD2 A:ASP88 3.3 45.1 1.0 OD1 A:ASP88 3.4 46.7 1.0 CB A:THR47 3.4 34.5 1.0 PG A:GTP301 3.4 38.7 1.0 O3B A:GTP301 3.6 34.9 1.0 CG A:ASP88 3.7 44.2 1.0 O1B A:GTP301 3.8 40.7 1.0 N A:THR47 3.8 39.4 1.0 CG2 A:THR65 3.9 34.8 1.0 N A:THR65 3.9 38.1 1.0 O2G A:GTP301 4.0 45.2 1.0 CA A:THR65 4.0 34.6 1.0 CA A:THR47 4.1 36.4 1.0 O A:THR89 4.3 33.0 1.0 CG2 A:THR47 4.3 37.7 1.0 O3A A:GTP301 4.5 36.1 1.0 O2A A:GTP301 4.5 38.7 1.0 O3G A:GTP301 4.6 38.8 1.0 CB A:LYS46 4.7 37.0 1.0 CE A:LYS46 4.7 38.3 1.0 O A:GLU63 4.7 49.0 1.0 C A:LYS46 4.8 35.9 1.0 PA A:GTP301 4.9 39.7 1.0 O1A A:GTP301 4.9 37.7 1.0 NZ A:LYS46 4.9 40.8 1.0

Magnesium binding site 2 out of 6 in the The RAB33B-ATG16L1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The RAB33B-ATG16L1 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg300 b:38.9 occ:1.00 OG1 B:THR65 1.9 35.2 1.0 O2B B:GTP301 2.0 48.8 1.0 OG1 B:THR47 2.0 45.5 1.0 O1G B:GTP301 2.2 41.0 1.0 CB B:THR65 2.7 39.9 1.0 PB B:GTP301 3.2 45.3 1.0 OD1 B:ASP88 3.2 52.2 1.0 OD2 B:ASP88 3.3 51.1 1.0 CB B:THR47 3.4 44.9 1.0 PG B:GTP301 3.4 42.3 1.0 CG B:ASP88 3.6 50.8 1.0 O1B B:GTP301 3.6 45.6 1.0 CG2 B:THR65 3.7 40.5 1.0 O3B B:GTP301 3.8 39.3 1.0 N B:THR47 3.9 39.2 1.0 CA B:THR65 3.9 45.2 1.0 O2G B:GTP301 3.9 48.6 1.0 N B:THR65 3.9 42.6 1.0 CA B:THR47 4.1 38.9 1.0 O B:THR89 4.2 39.6 1.0 CG2 B:THR47 4.4 48.0 1.0 O2A B:GTP301 4.4 43.6 1.0 CE B:LYS46 4.5 41.9 1.0 O3A B:GTP301 4.5 41.7 1.0 CB B:LYS46 4.6 49.9 1.0 O3G B:GTP301 4.7 42.4 1.0 C B:LYS46 4.8 36.9 1.0 PA B:GTP301 4.9 45.4 1.0 O1A B:GTP301 4.9 43.5 1.0 O B:GLU63 4.9 56.8 1.0 OD2 B:ASP69 5.0 64.5 1.0

Magnesium binding site 3 out of 6 in the The RAB33B-ATG16L1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The RAB33B-ATG16L1 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg300 b:38.5 occ:1.00 OG1 C:THR65 1.9 36.0 1.0 O2B C:GTP301 2.1 47.0 1.0 OG1 C:THR47 2.1 37.6 1.0 O1G C:GTP301 2.2 39.9 1.0 CB C:THR65 2.6 38.8 1.0 OD1 C:ASP88 3.2 47.5 1.0 PB C:GTP301 3.3 42.6 1.0 OD2 C:ASP88 3.3 51.0 1.0 PG C:GTP301 3.5 40.3 1.0 CB C:THR47 3.5 38.8 1.0 CG2 C:THR65 3.6 42.1 1.0 CG C:ASP88 3.6 46.8 1.0 O1B C:GTP301 3.6 42.5 1.0 O3B C:GTP301 3.8 36.6 1.0 CA C:THR65 3.8 38.7 1.0 N C:THR65 3.9 42.2 1.0 O2G C:GTP301 3.9 46.4 1.0 N C:THR47 3.9 44.0 1.0 O C:THR89 4.1 37.9 1.0 CA C:THR47 4.2 43.2 1.0 CG2 C:THR47 4.4 38.5 1.0 CE C:LYS46 4.5 42.0 1.0 O3A C:GTP301 4.6 38.2 1.0 CB C:LYS46 4.6 38.6 1.0 O3G C:GTP301 4.7 40.4 1.0 O2A C:GTP301 4.7 41.5 1.0 C C:LYS46 4.9 41.3 1.0 O C:GLU63 4.9 52.5 1.0 OD2 C:ASP69 5.0 65.4 1.0

Magnesium binding site 4 out of 6 in the The RAB33B-ATG16L1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The RAB33B-ATG16L1 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg300 b:44.1 occ:1.00 O2B D:GTP301 2.0 49.5 1.0 OG1 D:THR65 2.1 45.0 1.0 OG1 D:THR47 2.1 44.5 1.0 O1G D:GTP301 2.4 39.6 1.0 CB D:THR65 2.7 40.5 1.0 OD1 D:ASP88 3.1 58.6 1.0 PB D:GTP301 3.2 44.1 1.0 OD2 D:ASP88 3.2 55.4 1.0 CB D:THR47 3.5 45.3 1.0 CG D:ASP88 3.5 55.8 1.0 O1B D:GTP301 3.5 44.1 1.0 CG2 D:THR65 3.5 42.8 1.0 PG D:GTP301 3.6 38.9 1.0 N D:THR47 3.8 46.3 1.0 O3B D:GTP301 3.9 36.1 1.0 O D:THR89 3.9 43.3 1.0 O2G D:GTP301 3.9 44.7 1.0 CA D:THR65 4.0 45.5 1.0 CA D:THR47 4.1 45.8 1.0 N D:THR65 4.2 47.8 1.0 CE D:LYS46 4.4 44.3 1.0 CB D:LYS46 4.4 51.5 1.0 CG2 D:THR47 4.4 49.8 1.0 O3A D:GTP301 4.5 40.2 1.0 O2A D:GTP301 4.7 44.0 1.0 C D:LYS46 4.7 43.5 1.0 O3G D:GTP301 4.9 37.3 1.0 CB D:ASP88 4.9 50.2 1.0 O D:ASP88 4.9 57.3 1.0 PA D:GTP301 5.0 45.5 1.0 C D:THR89 5.0 41.0 1.0 NZ D:LYS46 5.0 45.6 1.0

Magnesium binding site 5 out of 6 in the The RAB33B-ATG16L1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The RAB33B-ATG16L1 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg300 b:38.6 occ:1.00 OG1 E:THR65 2.0 56.0 1.0 OG1 E:THR47 2.0 49.0 1.0 O2B E:GTP301 2.0 52.3 1.0 O1G E:GTP301 2.1 44.0 1.0 CB E:THR65 2.8 51.7 1.0 OD2 E:ASP88 3.2 60.1 1.0 PB E:GTP301 3.3 47.8 1.0 CB E:THR47 3.4 51.9 1.0 OD1 E:ASP88 3.4 66.8 1.0 PG E:GTP301 3.4 44.4 1.0 CG E:ASP88 3.6 62.9 1.0 O3B E:GTP301 3.8 41.1 1.0 CG2 E:THR65 3.8 48.3 1.0 N E:THR47 3.8 53.1 1.0 O1B E:GTP301 3.9 48.0 1.0 O2G E:GTP301 4.0 50.6 1.0 N E:THR65 4.0 52.5 1.0 CA E:THR65 4.0 50.7 1.0 CA E:THR47 4.1 50.4 1.0 O E:THR89 4.2 47.3 1.0 O2A E:GTP301 4.3 46.5 1.0 CG2 E:THR47 4.4 59.6 1.0 O3G E:GTP301 4.6 43.9 1.0 O3A E:GTP301 4.6 43.7 1.0 CB E:LYS46 4.7 47.4 1.0 C E:LYS46 4.8 50.4 1.0 PA E:GTP301 4.9 48.0 1.0 CE E:LYS46 4.9 45.9 1.0 O E:GLU63 5.0 67.4 1.0 O1A E:GTP301 5.0 46.9 1.0

Magnesium binding site 6 out of 6 in the The RAB33B-ATG16L1 Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The RAB33B-ATG16L1 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg300 b:39.6 occ:1.00 O2B F:GTP301 1.9 49.6 1.0 O1G F:GTP301 2.0 42.5 1.0 OG1 F:THR47 2.0 49.9 1.0 OG1 F:THR65 2.0 49.5 1.0 CB F:THR65 3.0 47.5 1.0 PB F:GTP301 3.1 45.8 1.0 PG F:GTP301 3.2 43.5 1.0 OD1 F:ASP88 3.3 49.2 1.0 CB F:THR47 3.4 47.3 1.0 OD2 F:ASP88 3.4 48.7 1.0 O1B F:GTP301 3.5 46.1 1.0 O2G F:GTP301 3.6 49.9 1.0 O3B F:GTP301 3.6 40.0 1.0 N F:THR47 3.7 48.2 1.0 CG F:ASP88 3.7 48.3 1.0 CG2 F:THR65 4.0 47.5 1.0 CA F:THR47 4.0 43.5 1.0 N F:THR65 4.1 54.0 1.0 CA F:THR65 4.2 51.3 1.0 O F:THR89 4.3 47.0 1.0 CG2 F:THR47 4.4 52.1 1.0 CB F:LYS46 4.4 46.2 1.0 O3G F:GTP301 4.4 43.6 1.0 O3A F:GTP301 4.4 41.5 1.0 O2A F:GTP301 4.4 43.5 1.0 CE F:LYS46 4.6 51.0 1.0 C F:LYS46 4.7 42.2 1.0 PA F:GTP301 4.8 44.9 1.0 O1A F:GTP301 4.8 42.7 1.0 NZ F:LYS46 5.0 51.7 1.0 O F:GLU63 5.0 73.2 1.0 CA F:LYS46 5.0 40.2 1.0

J.Metje-Sprink, J.Groffmann, P.Neumann, B.Barg-Kues, R.Ficner, K.Kuhnel, A.M.Schalk, B.Binotti. Crystal Structure of the RAB33B/ATG16L1 Effector Complex. Sci Rep V. 10 12956 2020.
ISSN: ESSN 2045-2322
PubMed: 32737358
DOI: 10.1038/S41598-020-69637-0