Magnesium in PDB 7ezb: Thorarchaeota Rab Bound to Gdp

The structure of Thorarchaeota Rab Bound to Gdp, PDB code: 7ezb was solved by R.C.Robinson, L.T.Tran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.20 / 1.50
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	68.791, 68.791, 66.346, 90, 90, 120
R / Rfree (%)	15.4 / 17.4

The binding sites of Magnesium atom in the Thorarchaeota Rab Bound to Gdp (pdb code 7ezb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thorarchaeota Rab Bound to Gdp, PDB code: 7ezb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Thorarchaeota Rab Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thorarchaeota Rab Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:15.3 occ:0.41 O3B A:GDP200 2.0 13.7 1.0 O A:HOH348 2.1 24.0 1.0 OG1 A:THR20 2.3 17.8 1.0 O A:HOH302 2.5 31.6 1.0 PB A:GDP200 3.1 13.9 1.0 O1B A:GDP200 3.3 15.5 1.0 CB A:THR20 3.4 14.1 1.0 NE A:ARG37 3.5 85.4 1.0 CD A:ARG37 3.5 80.8 1.0 CZ A:ARG37 3.7 84.0 1.0 OD2 A:ASP63 4.0 54.6 1.0 N A:THR20 4.0 12.6 1.0 NH2 A:ARG37 4.0 81.1 1.0 O1A A:GDP200 4.1 16.7 1.0 O3A A:GDP200 4.2 13.5 1.0 O2B A:GDP200 4.2 14.2 1.0 CA A:THR20 4.3 12.7 1.0 NH1 A:ARG37 4.4 86.3 1.0 O A:LEU64 4.4 49.8 1.0 PA A:GDP200 4.5 14.6 1.0 CG2 A:THR20 4.5 16.2 1.0 O2A A:GDP200 4.6 15.8 1.0 OD1 A:ASP63 4.6 43.6 1.0 CG A:ASP63 4.6 43.8 1.0 O A:HOH366 4.7 24.1 1.0 O A:HOH397 4.8 27.6 1.0 CG A:ARG37 5.0 77.0 1.0 CB A:LYS19 5.0 12.4 1.0 CE A:LYS19 5.0 15.2 1.0

Magnesium binding site 2 out of 2 in the Thorarchaeota Rab Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thorarchaeota Rab Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:23.5 occ:0.47 O B:HOH304 2.0 25.8 1.0 O3B B:GDP200 2.2 14.7 1.0 OG1 B:THR20 2.3 21.2 1.0 O B:HOH370 2.4 34.0 1.0 O B:HOH365 2.5 43.0 1.0 PB B:GDP200 3.3 14.4 1.0 O2B B:GDP200 3.4 16.5 1.0 CB B:THR20 3.5 16.6 1.0 OD2 B:ASP63 3.5 31.2 0.4 OD2 B:ASP63 4.1 34.2 0.6 N B:THR20 4.1 11.4 1.0 O2A B:GDP200 4.2 19.6 1.0 O3A B:GDP200 4.4 13.7 1.0 CA B:THR20 4.4 13.9 1.0 O1B B:GDP200 4.4 14.0 1.0 O B:HOH310 4.4 41.9 1.0 O B:HOH339 4.4 43.8 1.0 CG2 B:THR20 4.5 18.1 1.0 CG B:ASP63 4.6 26.5 0.4 PA B:GDP200 4.6 15.7 1.0 O B:LEU64 4.7 27.3 1.0 O1A B:GDP200 4.7 16.6 1.0 O B:HOH381 4.8 31.9 1.0 CG B:ASP63 4.9 28.1 0.6 OD1 B:ASP63 5.0 27.9 0.4 O B:HOH356 5.0 28.1 1.0

R.C.Robinson, L.T.Tran. Structure of Thor-Rab To Be Published.