Magnesium in PDB 1r4a: Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex

The structure of Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex, PDB code: 1r4a was solved by M.Wu, L.Lu, W.Hong, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.083, 86.924, 86.246, 118.11, 99.65, 95.47
R / Rfree (%)	24.6 / 26

The binding sites of Magnesium atom in the Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex (pdb code 1r4a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex, PDB code: 1r4a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex


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 Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:54.8 occ:1.00 OG1 A:THR31 2.5 16.4 1.0 O2G A:GNP1201 2.6 37.6 1.0 O2B A:GNP1201 2.6 42.4 1.0 OG1 A:THR48 2.8 25.5 1.0 O2A A:GNP1201 2.9 45.5 1.0 O A:ILE46 2.9 15.7 1.0 CB A:THR31 3.2 21.2 1.0 OG1 A:THR45 3.5 27.1 1.0 N3B A:GNP1201 3.5 42.9 1.0 PB A:GNP1201 3.5 43.6 1.0 PG A:GNP1201 3.7 43.1 1.0 N A:THR48 3.7 21.9 1.0 PA A:GNP1201 3.9 46.2 1.0 C A:ILE46 3.9 18.0 1.0 CG2 A:THR31 3.9 20.0 1.0 CB A:THR48 4.0 22.7 1.0 O3A A:GNP1201 4.0 39.8 1.0 O A:HOH1222 4.1 40.6 1.0 C A:PRO47 4.1 22.7 1.0 CA A:PRO47 4.1 21.2 1.0 O1A A:GNP1201 4.4 35.5 1.0 CA A:THR48 4.4 22.5 1.0 N A:PRO47 4.5 20.5 1.0 O1G A:GNP1201 4.5 42.5 1.0 CA A:THR31 4.5 19.5 1.0 N A:THR31 4.6 20.9 1.0 CB A:THR45 4.6 21.4 1.0 CG2 A:THR45 4.6 20.0 1.0 N A:ILE46 4.7 18.1 1.0 O3G A:GNP1201 4.8 38.6 1.0 O A:HOH1203 4.9 36.7 1.0 O1B A:GNP1201 4.9 44.5 1.0 O A:PRO47 5.0 22.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex


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 Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:39.9 occ:1.00 O B:HOH1203 2.5 30.6 1.0 OG1 B:THR31 2.5 20.9 1.0 O2G B:GNP1202 2.5 34.1 1.0 OG1 B:THR48 2.6 19.6 1.0 O2B B:GNP1202 2.7 33.0 1.0 O2A B:GNP1202 3.0 40.5 1.0 CB B:THR31 3.2 19.6 1.0 O B:ILE46 3.2 20.2 1.0 N3B B:GNP1202 3.6 36.8 1.0 PB B:GNP1202 3.7 34.2 1.0 PG B:GNP1202 3.7 32.6 1.0 N B:THR48 3.7 20.8 1.0 CB B:THR48 3.7 19.0 1.0 PA B:GNP1202 4.0 40.4 1.0 CG2 B:THR31 4.0 19.7 1.0 O3A B:GNP1202 4.1 38.9 1.0 OG1 B:THR45 4.1 29.5 1.0 C B:ILE46 4.2 19.6 1.0 CA B:THR48 4.3 18.9 1.0 O1A B:GNP1202 4.3 34.4 1.0 C B:PRO47 4.4 21.4 1.0 CA B:PRO47 4.4 20.2 1.0 CA B:THR31 4.5 19.0 1.0 CG2 B:THR45 4.5 18.1 1.0 O1G B:GNP1202 4.5 27.3 1.0 N B:THR31 4.6 20.3 1.0 O3G B:GNP1202 4.7 27.4 1.0 N B:PRO47 4.7 21.4 1.0 OD2 B:ASP67 4.9 23.6 1.0 CG2 B:THR48 4.9 22.7 1.0 CB B:THR45 4.9 21.4 1.0 N B:ILE46 4.9 20.6 1.0 O B:HOH1205 5.0 37.5 1.0 O1B B:GNP1202 5.0 37.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg903 b:39.0 occ:1.00 OG1 C:THR48 2.5 18.7 1.0 OG1 C:THR31 2.6 16.9 1.0 O2G C:GNP1203 2.7 28.1 1.0 O2B C:GNP1203 2.8 30.3 1.0 O C:HOH1260 2.8 29.5 1.0 O C:ILE46 3.1 17.8 1.0 CB C:THR31 3.1 19.1 1.0 O2A C:GNP1203 3.2 30.1 1.0 N C:THR48 3.6 20.5 1.0 CB C:THR48 3.7 19.9 1.0 PB C:GNP1203 3.8 32.0 1.0 N3B C:GNP1203 3.8 34.6 1.0 PG C:GNP1203 3.8 33.5 1.0 CG2 C:THR31 3.8 18.4 1.0 O C:HOH1228 3.9 31.9 1.0 OG1 C:THR45 3.9 31.8 1.0 C C:ILE46 4.1 17.9 1.0 PA C:GNP1203 4.1 33.5 1.0 CA C:THR48 4.2 20.1 1.0 C C:PRO47 4.2 19.0 1.0 O3A C:GNP1203 4.2 30.4 1.0 CA C:PRO47 4.3 16.4 1.0 CA C:THR31 4.5 19.4 1.0 O1A C:GNP1203 4.5 32.0 1.0 CG2 C:THR45 4.6 16.1 1.0 N C:THR31 4.6 19.8 1.0 N C:PRO47 4.6 19.0 1.0 O1G C:GNP1203 4.7 28.5 1.0 O C:HOH1241 4.8 38.2 1.0 O3G C:GNP1203 4.8 29.8 1.0 O C:HOH1215 4.8 26.0 1.0 N C:ILE46 4.8 20.1 1.0 OD2 C:ASP67 4.8 17.5 1.0 CB C:THR45 4.9 22.8 1.0 CG2 C:THR48 4.9 21.9 1.0 O C:HOH1248 5.0 41.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (ARL1) and Grip Domain of GOLGIN245 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg904 b:41.8 occ:1.00 OG1 D:THR48 2.4 23.0 1.0 O2B D:GNP1204 2.5 34.3 1.0 OG1 D:THR31 2.5 19.2 1.0 O2G D:GNP1204 2.6 34.4 1.0 CB D:THR31 3.0 18.8 1.0 O2A D:GNP1204 3.2 32.0 1.0 O D:ILE46 3.3 17.0 1.0 PB D:GNP1204 3.5 30.4 1.0 N3B D:GNP1204 3.6 33.4 1.0 PG D:GNP1204 3.7 31.8 1.0 CB D:THR48 3.7 20.8 1.0 N D:THR48 3.7 19.9 1.0 CG2 D:THR31 3.8 20.0 1.0 PA D:GNP1204 4.0 38.0 1.0 O3A D:GNP1204 4.1 35.6 1.0 OG1 D:THR45 4.2 21.3 1.0 CA D:THR48 4.3 21.1 1.0 C D:ILE46 4.3 18.2 1.0 C D:PRO47 4.4 19.6 1.0 CA D:THR31 4.4 17.8 1.0 O1A D:GNP1204 4.5 31.4 1.0 CA D:PRO47 4.5 18.0 1.0 N D:THR31 4.5 17.7 1.0 O D:HOH1213 4.6 39.0 1.0 O1G D:GNP1204 4.6 29.8 1.0 CG2 D:THR45 4.6 16.0 1.0 O3G D:GNP1204 4.7 28.0 1.0 CG2 D:THR48 4.7 24.3 1.0 N D:PRO47 4.8 18.8 1.0 O1B D:GNP1204 4.8 32.9 1.0 OD2 D:ASP67 4.9 15.3 1.0 O D:HOH1263 4.9 44.0 1.0

M.Wu, L.Lu, W.Hong, H.Song. Structural Basis For Recruitment of Grip Domain Golgin-245 By Small Gtpase ARL1. Nat.Struct.Mol.Biol. V. 11 86 2004.
ISSN: ISSN 1545-9993
PubMed: 14718928
DOI: 10.1038/NSMB714