Magnesium in PDB 1upt: Structure of A Complex of the Golgin-245 Grip Domain with ARL1

The structure of Structure of A Complex of the Golgin-245 Grip Domain with ARL1, PDB code: 1upt was solved by B.Panic, O.Perisic, D.B.Veprintsev, R.L.Williams, S.Munro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.42 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.497, 89.711, 72.534, 90.00, 110.69, 90.00
R / Rfree (%)	22.1 / 25.2

The binding sites of Magnesium atom in the Structure of A Complex of the Golgin-245 Grip Domain with ARL1 (pdb code 1upt). 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 A Complex of the Golgin-245 Grip Domain with ARL1, PDB code: 1upt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of A Complex of the Golgin-245 Grip Domain with ARL1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Complex of the Golgin-245 Grip Domain with ARL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1183 b:22.9 occ:1.00 O2G A:GTP1182 1.8 23.2 1.0 O A:HOH2007 2.0 21.2 1.0 OG1 A:THR31 2.0 22.7 1.0 O A:HOH2003 2.1 26.3 1.0 OG1 A:THR48 2.2 28.4 1.0 O2B A:GTP1182 2.2 20.4 1.0 PG A:GTP1182 3.0 26.0 1.0 CB A:THR48 3.1 32.0 1.0 PB A:GTP1182 3.2 23.7 1.0 CB A:THR31 3.2 23.4 1.0 O3B A:GTP1182 3.4 24.2 1.0 O3G A:GTP1182 3.5 23.9 1.0 N A:THR48 3.8 33.1 1.0 OD2 A:ASP67 4.1 33.5 1.0 N A:THR31 4.1 22.8 1.0 CA A:THR48 4.1 32.4 1.0 O2A A:GTP1182 4.1 26.3 1.0 OD1 A:ASP67 4.1 30.1 1.0 CG2 A:THR48 4.2 31.0 1.0 CG2 A:THR31 4.2 25.2 1.0 CA A:THR31 4.2 23.4 1.0 O A:ILE46 4.3 35.5 1.0 O1B A:GTP1182 4.3 23.8 1.0 O1G A:GTP1182 4.3 29.5 1.0 O3A A:GTP1182 4.3 24.2 1.0 PA A:GTP1182 4.6 26.1 1.0 CG A:ASP67 4.6 29.6 1.0 O1A A:GTP1182 4.8 19.7 1.0 C A:PRO47 4.8 34.6 1.0 NZ A:LYS30 4.9 23.3 1.0

Magnesium binding site 2 out of 4 in the Structure of A Complex of the Golgin-245 Grip Domain with ARL1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Complex of the Golgin-245 Grip Domain with ARL1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1182 b:22.0 occ:1.00 O2G C:GTP1181 1.9 22.4 1.0 OG1 C:THR31 2.0 20.9 1.0 O C:HOH2032 2.0 19.6 1.0 O2B C:GTP1181 2.1 20.0 1.0 O C:HOH2013 2.1 21.0 1.0 OG1 C:THR48 2.2 19.6 1.0 PG C:GTP1181 3.1 23.4 1.0 CB C:THR48 3.1 22.6 1.0 CB C:THR31 3.2 21.7 1.0 PB C:GTP1181 3.3 22.2 1.0 O3B C:GTP1181 3.5 21.8 1.0 O3G C:GTP1181 3.7 22.9 1.0 N C:THR48 3.8 22.6 1.0 N C:THR31 4.0 22.8 1.0 OD2 C:ASP67 4.0 25.4 1.0 CG2 C:THR31 4.1 24.2 1.0 CA C:THR48 4.1 22.9 1.0 O2A C:GTP1181 4.1 26.1 1.0 CG2 C:THR48 4.1 23.7 1.0 OD1 C:ASP67 4.2 28.0 1.0 CA C:THR31 4.2 23.0 1.0 O C:HOH2009 4.2 25.2 1.0 O3A C:GTP1181 4.3 22.3 1.0 O1B C:GTP1181 4.3 22.5 1.0 O C:ILE46 4.4 26.8 1.0 O1G C:GTP1181 4.4 24.6 1.0 PA C:GTP1181 4.5 23.4 1.0 CG C:ASP67 4.6 26.5 1.0 O1A C:GTP1181 4.7 25.9 1.0 C C:PRO47 4.8 24.4 1.0 CB C:LYS30 4.9 22.9 1.0 OD1 C:ASN52 4.9 30.2 1.0

Magnesium binding site 3 out of 4 in the Structure of A Complex of the Golgin-245 Grip Domain with ARL1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Complex of the Golgin-245 Grip Domain with ARL1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1182 b:17.6 occ:1.00 O2G E:GTP1181 2.0 17.1 1.0 O2B E:GTP1181 2.1 14.4 1.0 OG1 E:THR31 2.1 13.0 1.0 O E:HOH2032 2.1 18.3 1.0 O E:HOH2093 2.1 14.3 1.0 OG1 E:THR48 2.2 15.5 1.0 CB E:THR48 3.1 18.0 1.0 CB E:THR31 3.2 14.4 1.0 PG E:GTP1181 3.2 17.5 1.0 PB E:GTP1181 3.3 16.5 1.0 O3B E:GTP1181 3.5 17.1 1.0 O3G E:GTP1181 3.8 18.4 1.0 N E:THR48 3.8 20.4 1.0 OD2 E:ASP67 4.0 19.2 1.0 N E:THR31 4.0 14.4 1.0 O2A E:GTP1181 4.0 16.2 1.0 CA E:THR48 4.1 19.5 1.0 O E:HOH2016 4.1 16.2 1.0 CG2 E:THR31 4.1 12.9 1.0 CG2 E:THR48 4.2 17.9 1.0 CA E:THR31 4.2 14.7 1.0 O E:ILE46 4.2 23.1 1.0 OD1 E:ASP67 4.2 19.7 1.0 O3A E:GTP1181 4.3 15.2 1.0 O1B E:GTP1181 4.4 15.3 1.0 O1G E:GTP1181 4.4 21.2 1.0 PA E:GTP1181 4.6 15.0 1.0 CG E:ASP67 4.6 20.6 1.0 O1A E:GTP1181 4.7 13.9 1.0 C E:PRO47 4.7 21.4 1.0 OD1 E:ASN52 4.8 21.8 1.0 CA E:PRO47 4.9 22.3 1.0 CB E:LYS30 5.0 14.9 1.0

Magnesium binding site 4 out of 4 in the Structure of A Complex of the Golgin-245 Grip Domain with ARL1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Complex of the Golgin-245 Grip Domain with ARL1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1182 b:19.8 occ:1.00 OG1 G:THR31 2.0 21.4 1.0 O2G G:GTP1181 2.0 22.7 1.0 O2B G:GTP1181 2.0 19.4 1.0 O G:HOH2005 2.0 21.7 1.0 O G:HOH2053 2.1 22.1 1.0 OG1 G:THR48 2.2 22.0 1.0 CB G:THR31 3.1 22.3 1.0 PG G:GTP1181 3.1 23.0 1.0 CB G:THR48 3.2 23.3 1.0 PB G:GTP1181 3.2 20.7 1.0 O3B G:GTP1181 3.4 22.3 1.0 O3G G:GTP1181 3.7 24.2 1.0 N G:THR48 3.9 24.3 1.0 CG2 G:THR31 4.0 23.0 1.0 N G:THR31 4.0 22.6 1.0 OD2 G:ASP67 4.0 27.6 1.0 O2A G:GTP1181 4.1 24.6 1.0 CA G:THR48 4.2 23.1 1.0 CA G:THR31 4.2 23.0 1.0 OD1 G:ASP67 4.2 27.3 1.0 O G:ILE46 4.2 29.6 1.0 O3A G:GTP1181 4.2 22.3 1.0 CG2 G:THR48 4.2 22.4 1.0 O1B G:GTP1181 4.2 17.1 1.0 O G:HOH2010 4.3 23.9 1.0 O1G G:GTP1181 4.4 23.1 1.0 PA G:GTP1181 4.5 23.9 1.0 CG G:ASP67 4.6 25.1 1.0 O1A G:GTP1181 4.7 24.5 1.0 C G:PRO47 4.9 25.3 1.0 CB G:LYS30 5.0 21.6 1.0

B.Panic, O.Perisic, D.B.Veprintsev, R.L.Williams, S.Munro. Structural Basis For ARL1-Dependent Targeting of Homodimeric Grip Domains to the Golgi Apparatus Mol.Cell V. 12 863 2003.
ISSN: ISSN 1097-2765
PubMed: 14580338
DOI: 10.1016/S1097-2765(03)00356-3