Magnesium in PDB 5lxi: Gabarap-L1 ATG4B Lir Complex

The structure of Gabarap-L1 ATG4B Lir Complex, PDB code: 5lxi was solved by S.Mouilleron, M.Skytte Rasmussen, B.Kumar Shrestha, M.Wirth, K.Bowitzlarsen, Y.Abudu Princely, E.Sjottem, S.Tooze, T.Lamark, T.Johansen, R.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.21 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.888, 72.377, 30.620, 90.00, 99.21, 90.00
R / Rfree (%)	19.7 / 23

The binding sites of Magnesium atom in the Gabarap-L1 ATG4B Lir Complex (pdb code 5lxi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Gabarap-L1 ATG4B Lir Complex, PDB code: 5lxi:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Gabarap-L1 ATG4B Lir Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gabarap-L1 ATG4B Lir Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:27.1 occ:1.00 O D:HOH343 2.0 28.8 1.0 O D:HOH317 2.1 26.5 1.0 O D:HOH304 2.1 31.0 1.0 O D:HOH340 2.2 25.5 1.0 NE2 D:HIS69 2.2 19.0 1.0 CE1 D:HIS69 3.0 20.2 1.0 CD2 D:HIS69 3.3 17.0 1.0 OD2 D:ASP45 3.7 51.2 1.0 O D:HOH316 4.0 27.6 1.0 O D:ARG67 4.1 17.7 1.0 ND1 D:HIS69 4.2 20.1 1.0 CG D:HIS69 4.4 18.7 1.0 CG D:ASP45 4.5 47.8 1.0 O D:HOH301 4.9 21.0 1.0

Magnesium binding site 2 out of 3 in the Gabarap-L1 ATG4B Lir Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gabarap-L1 ATG4B Lir Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:38.9 occ:1.00 O B:HOH313 1.9 39.9 1.0 O B:HOH308 2.0 33.3 1.0 O B:HOH336 2.2 43.8 1.0 NE2 B:HIS69 2.3 35.6 1.0 O B:HOH320 2.3 34.8 1.0 CE1 B:HIS69 2.9 35.6 1.0 CD2 B:HIS69 3.5 36.3 1.0 O B:ARG67 3.8 26.5 1.0 ND1 B:HIS69 4.1 35.1 1.0 OD2 B:ASP45 4.2 67.5 1.0 CG B:HIS69 4.4 34.8 1.0 C B:ARG67 4.7 26.6 1.0 CG B:ASP45 4.9 61.8 1.0

Magnesium binding site 3 out of 3 in the Gabarap-L1 ATG4B Lir Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gabarap-L1 ATG4B Lir Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:35.4 occ:1.00 O B:HOH332 2.0 39.6 1.0 OD2 B:ASP54 2.0 30.1 1.0 O B:HOH323 2.0 39.3 1.0 O B:HOH306 2.2 67.8 1.0 O B:HOH302 2.2 41.0 1.0 CG B:ASP54 3.1 29.5 1.0 OD1 B:ASP54 3.6 33.1 1.0 OD2 B:ASP27 4.0 21.6 0.6 OD1 B:ASP27 4.1 25.8 0.6 O B:HOH329 4.3 26.0 1.0 CB B:ASP54 4.4 24.5 1.0 CG B:ASP27 4.5 22.1 0.6 OD1 B:ASP27 4.9 20.9 0.4

M.Skytte Rasmussen, S.Mouilleron, B.Kumar Shrestha, M.Wirth, R.Lee, K.Bowitz Larsen, Y.Abudu Princely, N.O'reilly, E.Sjttem, S.A.Tooze, T.Lamark, T.Johansen. ATG4B Contains A C-Terminal Lir Motif Important For Binding and Efficient Cleavage of Mammalian Orthologs of Yeast ATG8. Autophagy V. 13 834 2017.
ISSN: ESSN 1554-8635
PubMed: 28287329
DOI: 10.1080/15548627.2017.1287651