Magnesium in PDB 3lw8: Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A)

The structure of Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A), PDB code: 3lw8 was solved by B.U.Klink, S.Barden, T.V.Heidler, C.Borchers, M.Ladwein, T.E.B.Stradal, K.Rottner, D.W.Heinz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.20 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.590, 101.600, 97.030, 90.00, 96.43, 90.00
R / Rfree (%)	17.7 / 23.3

The binding sites of Magnesium atom in the Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A) (pdb code 3lw8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A), PDB code: 3lw8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:21.4 occ:1.00 O2B A:GDP201 2.0 14.1 1.0 O A:HOH1844 2.1 10.8 1.0 O A:HOH1739 2.1 13.9 1.0 OG1 A:THR19 2.1 11.8 1.0 O A:HOH1676 2.1 19.3 1.0 O A:HOH1337 2.2 12.5 1.0 CB A:THR19 3.2 10.9 1.0 PB A:GDP201 3.3 17.1 1.0 O1B A:GDP201 3.4 17.0 1.0 N A:THR19 3.9 10.8 1.0 OD2 A:ASP59 3.9 13.5 1.0 CA A:THR19 4.1 10.7 1.0 O1A A:GDP201 4.1 16.5 1.0 O F:HOH201 4.2 19.4 1.0 O3B A:GDP201 4.2 16.8 1.0 OD1 A:ASP59 4.3 9.5 1.0 O A:HOH217 4.3 20.3 1.0 O A:HOH214 4.3 18.6 1.0 CG2 A:THR19 4.3 7.8 1.0 O A:HOH212 4.3 17.6 1.0 O3A A:GDP201 4.3 16.2 1.0 O A:HOH215 4.4 21.6 1.0 CG A:ASP59 4.5 13.2 1.0 PA A:GDP201 4.6 17.0 1.0 O A:THR60 4.7 15.9 1.0 O2A A:GDP201 4.8 15.8 1.0 CB A:LYS18 4.8 8.9 1.0 O A:HOH184 4.9 14.7 1.0 C A:LYS18 5.0 10.6 1.0 NZ A:LYS18 5.0 17.8 1.0

Magnesium binding site 2 out of 4 in the Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:26.7 occ:1.00 O3B B:GDP201 2.0 19.1 1.0 O B:HOH1677 2.0 18.1 1.0 O B:HOH1851 2.1 19.0 1.0 OG1 B:THR19 2.1 13.7 1.0 O B:HOH1740 2.2 14.3 1.0 O B:HOH810 2.3 19.9 1.0 CB B:THR19 3.2 13.1 1.0 PB B:GDP201 3.2 22.9 1.0 O1B B:GDP201 3.4 24.2 1.0 N B:THR19 3.8 13.1 1.0 O B:HOH198 4.0 23.4 1.0 OD2 B:ASP59 4.0 11.6 1.0 CA B:THR19 4.1 13.2 1.0 O1A B:GDP201 4.1 21.5 1.0 O G:HOH1852 4.1 24.5 1.0 O2B B:GDP201 4.2 21.2 1.0 OD1 B:ASP59 4.2 15.5 1.0 CG2 B:THR19 4.3 12.8 1.0 O3A B:GDP201 4.3 19.6 1.0 O B:HOH454 4.4 25.3 1.0 O B:HOH234 4.4 15.5 1.0 O B:HOH186 4.4 19.8 1.0 O B:HOH197 4.5 30.3 1.0 CG B:ASP59 4.5 14.6 1.0 PA B:GDP201 4.6 20.7 1.0 O2A B:GDP201 4.7 17.7 1.0 O B:THR60 4.8 21.1 1.0 CB B:LYS18 4.9 13.5 1.0 O B:HOH927 4.9 33.0 1.0 NZ B:LYS18 4.9 15.0 1.0 C B:LYS18 4.9 13.2 1.0

Magnesium binding site 3 out of 4 in the Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:18.5 occ:1.00 O2B C:GDP201 2.0 14.4 1.0 OG1 C:THR19 2.1 10.0 1.0 O C:HOH1738 2.1 11.3 1.0 O C:HOH1853 2.1 11.6 1.0 O C:HOH210 2.2 13.3 1.0 O C:HOH1675 2.2 11.8 1.0 CB C:THR19 3.1 9.7 1.0 PB C:GDP201 3.2 17.3 1.0 O1B C:GDP201 3.4 19.9 1.0 O H:HOH206 3.9 14.2 1.0 OD2 C:ASP59 3.9 10.3 1.0 N C:THR19 3.9 8.4 1.0 CA C:THR19 4.1 9.6 1.0 O1A C:GDP201 4.1 19.0 1.0 O C:HOH238 4.2 20.7 1.0 CG2 C:THR19 4.2 9.9 1.0 O C:HOH218 4.2 18.4 1.0 O3B C:GDP201 4.2 16.0 1.0 O C:HOH188 4.3 22.3 1.0 OD1 C:ASP59 4.3 13.4 1.0 O3A C:GDP201 4.3 17.5 1.0 O C:HOH262 4.4 26.1 1.0 O C:HOH190 4.4 11.2 1.0 CG C:ASP59 4.5 13.3 1.0 PA C:GDP201 4.6 17.5 1.0 O C:THR60 4.8 14.1 1.0 O2A C:GDP201 4.8 14.2 1.0 NZ C:LYS18 4.8 13.0 1.0 CE C:LYS18 5.0 11.6 1.0

Magnesium binding site 4 out of 4 in the Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Shigella IPGB2 in Complex with Human Rhoa, Gdp and MG2+ (Complex A) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:30.2 occ:1.00 O2B D:GDP201 2.0 24.3 1.0 OG1 D:THR19 2.0 16.5 1.0 O D:HOH841 2.2 18.6 1.0 O D:HOH1742 2.2 20.2 1.0 O D:HOH1470 2.2 25.5 1.0 O D:HOH1678 2.2 20.4 1.0 CB D:THR19 3.2 18.1 1.0 PB D:GDP201 3.2 27.8 1.0 O1B D:GDP201 3.5 28.0 1.0 N D:THR19 3.9 16.9 1.0 O E:HOH198 4.0 22.1 1.0 O1A D:GDP201 4.0 28.2 1.0 OD2 D:ASP59 4.0 19.3 1.0 O D:HOH403 4.1 20.3 1.0 CA D:THR19 4.1 17.6 1.0 O3B D:GDP201 4.2 25.9 1.0 CG2 D:THR19 4.3 17.1 1.0 O3A D:GDP201 4.3 26.5 1.0 O D:HOH272 4.4 32.4 1.0 O D:HOH679 4.4 26.1 1.0 O D:HOH290 4.4 25.9 1.0 OD1 D:ASP59 4.4 19.4 1.0 PA D:GDP201 4.5 27.2 1.0 O D:HOH184 4.6 20.0 1.0 CG D:ASP59 4.7 20.4 1.0 O2A D:GDP201 4.7 27.3 1.0 NZ D:LYS18 4.9 20.8 1.0 O D:THR60 4.9 24.3 1.0 CB D:LYS18 4.9 17.4 1.0 CE D:LYS18 4.9 18.8 1.0 C D:LYS18 5.0 17.3 1.0

B.U.Klink, S.Barden, T.V.Heidler, C.Borchers, M.Ladwein, T.E.B.Stradal, K.Rottner, D.W.Heinz. Structure of Shigella IPGB2 in Complex with Human Rhoa: Implications For the Mechanism of Bacterial Gef-Mimicry J.Biol.Chem. V. 285 17197 2010.
ISSN: ISSN 0021-9258
PubMed: 20363740
DOI: 10.1074/JBC.M110.107953