Magnesium in PDB 4i1o: Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3

The structure of Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3, PDB code: 4i1o was solved by E.M.Gazdag, A.Streller, I.R.Vetter, R.S.Goody, A.Itzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.16 / 2.70
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	124.410, 124.410, 147.470, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 24.9

The structure of Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 (pdb code 4i1o). 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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3, PDB code: 4i1o:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:33.0 occ:1.00 OG A:SER22 1.8 29.5 1.0 O3B A:GDP202 2.1 28.9 1.0 OG1 A:THR40 2.2 32.3 1.0 OD2 A:ASP63 2.3 47.5 1.0 O A:HOH306 2.9 21.8 1.0 CB A:THR40 3.1 25.1 1.0 CB A:SER22 3.2 28.9 1.0 F3 A:BEF203 3.3 26.9 1.0 CG A:ASP63 3.3 43.7 1.0 PB A:GDP202 3.4 32.9 1.0 BE A:BEF203 3.7 32.1 1.0 OD1 A:ASP63 3.7 45.6 1.0 N A:SER22 3.7 30.6 1.0 O2B A:GDP202 3.8 35.2 1.0 O A:THR64 3.8 30.7 1.0 CG2 A:THR40 3.8 24.9 1.0 CA A:SER22 3.9 30.7 1.0 O1B A:GDP202 4.0 32.2 1.0 F2 A:BEF203 4.2 51.8 1.0 CA A:THR40 4.3 27.7 1.0 N A:THR40 4.3 34.0 1.0 CB A:LYS21 4.4 27.9 1.0 CE A:LYS21 4.5 26.1 1.0 O A:HOH305 4.5 31.2 1.0 O3A A:GDP202 4.6 23.3 1.0 CB A:ASP63 4.6 39.4 1.0 O1A A:GDP202 4.7 33.0 1.0 C A:LYS21 4.7 33.9 1.0 C A:THR64 4.8 33.0 1.0 O2A A:GDP202 4.8 29.2 1.0 PA A:GDP202 4.9 33.2 1.0 NZ A:LYS21 4.9 27.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:34.5 occ:1.00 OG C:SER22 2.0 26.1 1.0 O C:HOH304 2.0 24.6 1.0 OG1 C:THR40 2.1 34.8 1.0 O3B C:GDP202 2.1 29.1 1.0 CB C:SER22 3.1 24.4 1.0 PB C:GDP202 3.2 32.8 1.0 CB C:THR40 3.3 25.8 1.0 F2 C:BEF203 3.4 27.2 1.0 BE C:BEF203 3.4 47.7 1.0 O2B C:GDP202 3.4 46.8 1.0 O2A C:GDP202 3.5 31.9 1.0 N C:THR40 3.5 34.6 1.0 O3A C:GDP202 3.8 22.2 1.0 HO4 C:PEG205 4.0 70.7 1.0 CA C:THR40 4.0 28.1 1.0 PA C:GDP202 4.0 36.4 1.0 H42 C:PEG205 4.1 78.9 1.0 NH2 B:ARG444 4.1 32.3 1.0 O1A C:GDP202 4.2 37.6 1.0 O4 C:PEG205 4.2 58.9 1.0 OD2 C:ASP63 4.2 45.4 1.0 F3 C:BEF203 4.2 59.2 1.0 CA C:SER22 4.3 27.0 1.0 N C:SER22 4.3 27.6 1.0 O C:ILE38 4.3 42.4 1.0 C C:SER39 4.4 34.2 1.0 CA C:SER39 4.4 31.6 1.0 CG2 C:THR40 4.4 23.3 1.0 O1B C:GDP202 4.5 28.8 1.0 F1 C:BEF203 4.6 45.8 1.0 C4 C:PEG205 4.6 65.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:32.6 occ:1.00 F2 E:BEF203 1.7 36.5 1.0 O E:HOH306 2.0 16.8 1.0 OG E:SER22 2.1 27.5 1.0 OG1 E:THR40 2.1 33.7 1.0 O1B E:GDP202 2.1 37.5 1.0 O2A E:GDP202 2.8 33.2 1.0 PB E:GDP202 3.1 34.4 1.0 CB E:SER22 3.2 24.2 1.0 O3B E:GDP202 3.2 29.1 1.0 BE E:BEF203 3.2 61.5 1.0 CB E:THR40 3.3 27.9 1.0 N E:THR40 3.4 34.8 1.0 O3A E:GDP202 3.7 26.3 1.0 PA E:GDP202 3.8 38.3 1.0 CA E:THR40 3.9 30.3 1.0 F1 E:BEF203 4.0 55.0 1.0 NH2 F:ARG444 4.0 33.1 1.0 O E:ILE38 4.0 45.2 1.0 F3 E:BEF203 4.2 66.4 1.0 N E:SER22 4.3 28.9 1.0 C E:SER39 4.3 35.5 1.0 CA E:SER22 4.4 28.7 1.0 O E:HOH313 4.4 37.3 1.0 OD2 E:ASP63 4.4 39.5 1.0 CA E:SER39 4.4 33.8 1.0 O2B E:GDP202 4.4 42.5 1.0 CG2 E:THR40 4.5 27.1 1.0 O1A E:GDP202 4.7 35.7 1.0 C E:ILE38 4.9 36.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg201 b:35.7 occ:1.00 O3B G:GDP202 2.0 40.1 1.0 OG G:SER22 2.0 25.7 1.0 O G:HOH307 2.0 28.9 1.0 OG1 G:THR40 2.1 34.7 1.0 CB G:SER22 3.0 22.5 1.0 O2A G:GDP202 3.1 30.6 1.0 PB G:GDP202 3.1 33.4 1.0 CB G:THR40 3.4 26.9 1.0 N G:THR40 3.4 33.1 1.0 BE G:BEF203 3.4 38.5 1.0 O2B G:GDP202 3.5 45.7 1.0 O3A G:GDP202 3.6 19.8 1.0 F1 G:BEF203 3.7 36.5 1.0 PA G:GDP202 3.8 38.7 1.0 CA G:THR40 3.9 28.1 1.0 NH2 H:ARG444 4.0 32.3 1.0 O G:ILE38 4.1 42.8 1.0 OD2 G:ASP63 4.2 39.2 1.0 CA G:SER22 4.3 28.0 1.0 F2 G:BEF203 4.3 0.1 1.0 C G:SER39 4.3 33.1 1.0 CA G:SER39 4.3 30.7 1.0 N G:SER22 4.3 30.4 1.0 O G:HOH314 4.4 30.0 1.0 O1B G:GDP202 4.4 33.8 1.0 CG2 G:THR40 4.5 24.7 1.0 F3 G:BEF203 4.5 57.1 1.0 O1A G:GDP202 4.6 41.2 1.0 C G:ILE38 4.9 34.5 1.0

E.Mihai Gazdag, A.Streller, I.Haneburger, H.Hilbi, I.R.Vetter, R.S.Goody, A.Itzen. Mechanism of RAB1B Deactivation By the Legionella Pneumophila Gap Lepb. Embo Rep. V. 14 199 2013.
ISSN: ISSN 1469-221X
PubMed: 23288104
DOI: 10.1038/EMBOR.2012.211