Magnesium in PDB 3bbp: RAB6-Gtp:GCC185 Rab Binding Domain Complex

The structure of RAB6-Gtp:GCC185 Rab Binding Domain Complex, PDB code: 3bbp was solved by A.Schweizer Burguete, T.D.Fenn, A.T.Brunger, S.R.Pfeffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.00
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	168.599, 168.599, 168.955, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 26.8

The binding sites of Magnesium atom in the RAB6-Gtp:GCC185 Rab Binding Domain Complex (pdb code 3bbp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the RAB6-Gtp:GCC185 Rab Binding Domain Complex, PDB code: 3bbp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the RAB6-Gtp:GCC185 Rab Binding Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RAB6-Gtp:GCC185 Rab Binding Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:74.7 occ:1.00 OG1 A:THR45 2.5 71.3 1.0 OG1 A:THR27 2.5 52.4 1.0 O2B A:GTP500 2.5 66.1 1.0 O3G A:GTP500 2.7 61.1 1.0 OD1 A:ASP68 2.8 70.8 1.0 CB A:THR45 3.1 82.0 1.0 O A:THR69 3.2 51.5 1.0 OD2 A:ASP68 3.3 67.1 1.0 CG A:ASP68 3.3 84.6 1.0 N A:THR27 3.5 75.2 1.0 CE A:LYS26 3.6 75.5 1.0 O1G A:GTP500 3.6 39.7 1.0 CG2 A:THR45 3.7 54.8 1.0 PG A:GTP500 3.7 87.5 1.0 CB A:THR27 3.7 91.2 1.0 CB A:LYS26 3.8 62.6 1.0 PB A:GTP500 3.9 68.8 1.0 CA A:THR27 4.0 35.8 1.0 NZ A:LYS26 4.0 60.6 1.0 O3B A:GTP500 4.3 76.6 1.0 C A:THR69 4.4 99.8 1.0 C A:LYS26 4.4 83.5 1.0 O1B A:GTP500 4.4 83.3 1.0 CA A:THR45 4.5 72.7 1.0 CG2 A:THR27 4.5 77.7 1.0 CA A:LYS26 4.6 57.1 1.0 CD A:LYS26 4.6 58.2 1.0 CB A:ASP68 4.6 54.4 1.0 CG A:LYS26 4.7 76.0 1.0 N A:THR45 4.7 0.3 1.0 C A:ASP68 4.8 96.6 1.0 O2A A:GTP500 4.9 69.9 1.0 N A:THR69 4.9 80.0 1.0 O A:ASP68 5.0 80.3 1.0 O2G A:GTP500 5.0 89.3 1.0

Magnesium binding site 2 out of 3 in the RAB6-Gtp:GCC185 Rab Binding Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RAB6-Gtp:GCC185 Rab Binding Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:67.5 occ:1.00 O2B B:GTP500 2.5 73.8 1.0 OG1 B:THR27 2.7 71.6 1.0 OG1 B:THR45 2.7 76.5 1.0 OD1 B:ASP68 2.8 0.5 1.0 O3G B:GTP500 2.9 71.8 1.0 O B:THR69 3.1 75.2 1.0 CE B:LYS26 3.3 88.7 1.0 CB B:THR45 3.3 88.2 1.0 CG B:ASP68 3.4 98.6 1.0 OD2 B:ASP68 3.4 96.7 1.0 O1G B:GTP500 3.5 58.9 1.0 N B:THR27 3.5 89.0 1.0 CB B:LYS26 3.6 64.8 1.0 PG B:GTP500 3.7 0.9 1.0 PB B:GTP500 3.8 91.2 1.0 NZ B:LYS26 3.8 76.1 1.0 CG2 B:THR45 3.9 55.8 1.0 CB B:THR27 3.9 98.2 1.0 CA B:THR27 4.1 51.4 1.0 O1B B:GTP500 4.2 84.5 1.0 C B:THR69 4.3 0.2 1.0 O3B B:GTP500 4.3 0.6 1.0 C B:LYS26 4.3 77.0 1.0 CD B:LYS26 4.3 75.8 1.0 CG B:LYS26 4.4 79.4 1.0 CA B:LYS26 4.5 70.2 1.0 CA B:THR45 4.7 80.3 1.0 CB B:ASP68 4.7 70.4 1.0 CG2 B:THR27 4.7 72.4 1.0 C B:ASP68 4.8 0.0 1.0 N B:THR69 4.9 93.2 1.0 N B:THR45 4.9 0.3 1.0 N B:LYS26 4.9 88.5 1.0 O2A B:GTP500 4.9 76.0 1.0 CA B:ALA70 5.0 99.0 1.0

Magnesium binding site 3 out of 3 in the RAB6-Gtp:GCC185 Rab Binding Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of RAB6-Gtp:GCC185 Rab Binding Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:77.4 occ:1.00 OG1 C:THR45 2.5 64.7 1.0 O2B C:GTP500 2.6 78.4 1.0 OG1 C:THR27 2.7 56.7 1.0 O3G C:GTP500 2.8 82.1 1.0 OD1 C:ASP68 2.9 0.5 1.0 O C:THR69 3.0 77.0 1.0 CB C:THR45 3.1 95.1 1.0 CG C:ASP68 3.4 98.8 1.0 CE C:LYS26 3.4 87.2 1.0 OD2 C:ASP68 3.4 82.8 1.0 O1G C:GTP500 3.5 63.1 1.0 CG2 C:THR45 3.6 70.8 1.0 PG C:GTP500 3.7 0.7 1.0 N C:THR27 3.7 77.4 1.0 CB C:LYS26 3.8 71.0 1.0 NZ C:LYS26 3.9 74.6 1.0 PB C:GTP500 3.9 0.6 1.0 CB C:THR27 4.0 0.0 1.0 C C:THR69 4.1 0.4 1.0 CA C:THR27 4.2 57.1 1.0 O3B C:GTP500 4.4 76.7 1.0 O1B C:GTP500 4.4 79.5 1.0 CA C:THR45 4.5 0.1 1.0 CD C:LYS26 4.5 84.6 1.0 C C:LYS26 4.5 95.8 1.0 CG C:LYS26 4.6 95.5 1.0 CB C:ASP68 4.7 76.3 1.0 CA C:LYS26 4.7 90.1 1.0 CG2 C:THR27 4.7 89.8 1.0 N C:THR45 4.7 0.2 1.0 C C:ASP68 4.7 0.5 1.0 N C:THR69 4.8 95.6 1.0 CA C:ALA70 4.8 75.8 1.0 O C:ASP68 4.9 98.5 1.0 N C:ALA70 4.9 0.5 1.0 O2G C:GTP500 5.0 92.7 1.0 O2A C:GTP500 5.0 75.4 1.0

A.S.Burguete, T.D.Fenn, A.T.Brunger, S.R.Pfeffer. Rab and Arl Gtpase Family Members Cooperate in the Localization of the Golgin GCC185. Cell(Cambridge,Mass.) V. 132 286 2008.
ISSN: ISSN 0092-8674
PubMed: 18243103
DOI: 10.1016/J.CELL.2007.11.048