Magnesium in PDB 5ee5: Structure of Human ARL1 in Complex with the Dcb Domain of BIG1

The structure of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1, PDB code: 5ee5 was solved by A.Galindo, N.Soler, S.Munro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.07 / 2.28
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.166, 50.727, 103.837, 90.00, 111.98, 90.00
R / Rfree (%)	21.7 / 25.9

The structure of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 also contains other interesting chemical elements:

Chlorine	(Cl)	7 atoms
Sodium	(Na)	14 atoms

The binding sites of Magnesium atom in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 (pdb code 5ee5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1, PDB code: 5ee5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


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 ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:43.8 occ:1.00 OG1 B:THR48 2.2 39.5 1.0 OG1 B:THR31 2.3 46.9 1.0 O1B B:GTP201 2.3 43.0 1.0 O1G B:GTP201 2.4 40.4 1.0 MG B:MG205 2.5 40.9 1.0 CB B:THR48 2.9 38.1 1.0 OD1 B:ASP67 3.2 43.5 1.0 PG B:GTP201 3.4 47.3 1.0 OD2 B:ASP67 3.4 39.9 1.0 O2G B:GTP201 3.5 40.4 1.0 CB B:THR31 3.6 46.6 1.0 PB B:GTP201 3.6 43.6 1.0 CG B:ASP67 3.7 44.5 1.0 CG2 B:THR48 3.7 39.2 1.0 O B:LEU68 3.9 42.4 1.0 N B:THR31 3.9 44.2 1.0 O3B B:GTP201 4.0 37.5 1.0 CE B:LYS30 4.1 41.4 1.0 NZ B:LYS30 4.1 43.3 1.0 O2B B:GTP201 4.2 46.6 1.0 CA B:THR48 4.2 38.2 1.0 N B:THR48 4.2 42.7 1.0 CA B:THR31 4.2 46.1 1.0 CB B:LYS30 4.3 46.8 1.0 C B:LEU68 4.6 38.2 1.0 CG2 B:THR31 4.6 44.7 1.0 CA B:GLY69 4.7 34.9 1.0 O B:HOH310 4.7 45.3 1.0 O3G B:GTP201 4.8 34.8 1.0 C B:LYS30 4.8 45.5 1.0 O3A B:GTP201 4.9 47.2 1.0 O2A B:GTP201 5.0 49.2 1.0 N B:GLY69 5.0 31.6 1.0 ND2 B:ASN52 5.0 43.1 1.0

Magnesium binding site 2 out of 4 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:64.9 occ:1.00 OD2 B:ASP96 2.5 57.9 1.0 OD2 B:ASP93 2.8 60.5 1.0 NH2 B:ARG99 3.1 54.0 1.0 CG B:ASP96 3.5 58.2 1.0 CB B:ASP93 3.6 48.5 1.0 CG B:ASP93 3.6 51.7 1.0 CB B:ASP96 3.8 56.7 1.0 O B:ASP26 3.9 48.1 1.0 CZ B:ARG99 4.2 63.8 1.0 C B:GLY27 4.3 49.4 1.0 O B:GLY27 4.4 47.0 1.0 CA B:GLY27 4.5 49.1 1.0 NE B:ARG99 4.5 59.7 1.0 OD1 B:ASP96 4.6 55.1 1.0 NZ B:LYS127 4.7 52.3 1.0 N B:ALA28 4.8 48.0 1.0 OD1 B:ASP93 4.8 49.5 1.0 O B:HOH309 4.9 45.5 1.0 C B:ASP26 4.9 52.7 1.0 CA B:ASP96 5.0 57.4 1.0

Magnesium binding site 3 out of 4 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:91.9 occ:1.00 O B:LEU61 2.2 0.8 1.0 CG2 B:THR57 2.4 98.8 1.0 CA B:THR57 2.7 90.7 1.0 CB B:THR57 2.9 93.4 1.0 C B:LEU61 2.9 98.2 1.0 N B:TYR58 3.0 97.8 1.0 C B:THR57 3.1 96.3 1.0 O B:TYR58 3.1 0.2 1.0 N B:LEU61 3.3 0.8 1.0 OG1 B:THR57 3.4 91.3 1.0 C B:TYR58 3.6 0.6 1.0 CA B:LEU61 3.7 0.8 1.0 N B:LYS62 3.7 97.0 1.0 O B:VAL56 3.8 79.0 1.0 C B:ASN60 3.9 0.3 1.0 CA B:TYR58 3.9 0.7 1.0 N B:THR57 3.9 83.7 1.0 CA B:LYS62 4.0 90.1 1.0 O B:THR57 4.1 99.2 1.0 CA B:ASN60 4.1 0.9 1.0 C B:VAL56 4.3 76.3 1.0 CD2 B:PHE63 4.4 87.1 1.0 N B:LYS59 4.5 0.1 1.0 CE2 B:PHE63 4.6 89.7 1.0 N B:PHE63 4.6 81.2 1.0 OD1 B:ASN60 4.7 0.9 1.0 C B:LYS62 4.7 84.8 1.0 O B:ASN60 4.8 0.5 1.0 CB B:LEU61 4.9 0.8 1.0 CG B:ASN60 4.9 0.3 1.0 CA B:LYS59 4.9 0.1 1.0 CB B:TYR58 5.0 98.8 1.0

Magnesium binding site 4 out of 4 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg205 b:40.9 occ:1.00 O1B B:GTP201 2.2 43.0 1.0 O1G B:GTP201 2.3 40.4 1.0 OG1 B:THR31 2.4 46.9 1.0 MG B:MG202 2.5 43.8 1.0 OG1 B:THR48 2.5 39.5 1.0 O2A B:GTP201 2.9 49.2 1.0 CB B:THR31 3.0 46.6 1.0 O B:ILE46 3.1 48.1 1.0 PB B:GTP201 3.2 43.6 1.0 PG B:GTP201 3.5 47.3 1.0 O3B B:GTP201 3.6 37.5 1.0 N B:THR48 3.7 42.7 1.0 PA B:GTP201 3.7 42.7 1.0 CB B:THR48 3.8 38.1 1.0 O3A B:GTP201 3.8 47.2 1.0 CG2 B:THR31 3.9 44.7 1.0 O B:HOH310 4.1 45.3 1.0 O1A B:GTP201 4.1 38.7 1.0 C B:ILE46 4.2 51.6 1.0 CA B:THR31 4.3 46.1 1.0 OG1 B:THR45 4.3 56.0 1.0 CA B:THR48 4.3 38.2 1.0 N B:THR31 4.3 44.2 1.0 CA B:PRO47 4.4 48.4 1.0 O B:HOH313 4.4 50.6 1.0 O3G B:GTP201 4.5 34.8 1.0 C B:PRO47 4.5 48.6 1.0 O2G B:GTP201 4.5 40.4 1.0 CB B:THR45 4.5 54.0 1.0 O2B B:GTP201 4.5 46.6 1.0 N B:PRO47 4.8 43.8 1.0 OD2 B:ASP67 4.9 39.9 1.0 CG2 B:THR48 4.9 39.2 1.0

A.Galindo, N.Soler, S.H.Mclaughlin, M.Yu, R.L.Williams, S.Munro. Structural Insights Into ARL1-Mediated Targeting of the Arf-Gef BIG1 to the Trans-Golgi. Cell Rep V. 16 839 2016.
ISSN: ESSN 2211-1247
PubMed: 27373159
DOI: 10.1016/J.CELREP.2016.06.022