Magnesium in PDB 2o52: Crystal Structure of Human RAB4B in Complex with Gdp

The structure of Crystal Structure of Human RAB4B in Complex with Gdp, PDB code: 2o52 was solved by H.Zhu, W.Tempel, J.Wang, Y.Shen, R.Landry, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.528, 67.528, 179.955, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of Human RAB4B in Complex with Gdp (pdb code 2o52). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human RAB4B in Complex with Gdp, PDB code: 2o52:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human RAB4B in Complex with Gdp


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 Human RAB4B in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:29.9 occ:1.00 O A:HOH1005 2.0 27.8 1.0 O A:HOH1004 2.1 30.6 1.0 O A:HOH1007 2.1 26.4 1.0 O A:HOH1006 2.2 34.8 1.0 O2B A:GDP601 2.2 34.0 1.0 OG A:SER22 2.2 31.7 1.0 CB A:SER22 3.3 34.9 1.0 PB A:GDP601 3.4 33.9 1.0 O3B A:GDP601 3.5 38.2 1.0 OD2 A:ASP63 3.8 32.0 1.0 N A:SER22 3.9 35.9 1.0 OD1 A:ASP63 4.1 31.9 1.0 OG1 A:THR64 4.1 26.1 1.0 CA A:SER22 4.2 36.9 1.0 O2A A:GDP601 4.3 33.9 1.0 O1B A:GDP601 4.3 31.0 1.0 OE2 A:GLU68 4.3 30.7 1.0 CG A:ASP63 4.4 29.5 1.0 N A:GLY66 4.4 34.4 1.0 O3A A:GDP601 4.5 36.2 1.0 O A:HOH1008 4.6 25.4 1.0 CA A:GLY66 4.7 31.3 1.0 PA A:GDP601 4.7 33.0 1.0 NZ A:LYS21 4.8 26.1 1.0 CB A:LYS21 4.8 33.1 1.0 O1A A:GDP601 4.8 33.1 1.0 CE A:LYS21 4.8 27.7 1.0 C A:LYS21 4.9 37.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human RAB4B in Complex with Gdp


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 Human RAB4B in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:33.1 occ:1.00 O B:HOH604 2.1 35.1 1.0 OG B:SER22 2.2 34.7 1.0 O2B B:GDP601 2.2 29.8 1.0 O B:HOH605 2.2 31.3 1.0 O B:HOH606 2.2 38.2 1.0 O B:HOH607 2.2 25.9 1.0 CB B:SER22 3.2 34.7 1.0 PB B:GDP601 3.3 29.5 1.0 O3B B:GDP601 3.5 31.0 1.0 N B:SER22 3.9 30.3 1.0 OD2 B:ASP63 4.0 33.2 1.0 O2A B:GDP601 4.1 34.2 1.0 OD1 B:ASP63 4.1 28.5 1.0 CA B:SER22 4.1 29.0 1.0 OG1 B:THR64 4.2 28.3 1.0 O1B B:GDP601 4.3 26.4 1.0 NH2 B:ARG69 4.3 55.5 1.0 OE2 B:GLU68 4.4 30.6 1.0 O3A B:GDP601 4.4 28.4 1.0 CG B:ASP63 4.4 29.4 1.0 N B:GLY66 4.5 35.4 1.0 PA B:GDP601 4.6 30.9 1.0 O B:HOH609 4.7 26.0 1.0 CA B:GLY66 4.7 32.0 1.0 O1A B:GDP601 4.7 26.1 1.0 CB B:LYS21 4.8 26.8 1.0 NZ B:LYS21 4.9 23.3 1.0 CE B:LYS21 4.9 25.0 1.0 C B:LYS21 4.9 29.9 1.0 CZ B:ARG69 5.0 57.6 1.0

H.Zhu, W.Tempel, J.Wang, Y.Shen, R.Landry, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park. Crystal Structure of Human RAB4B in Complex with Gdp To Be Published.