Magnesium in PDB 4fmc: Espg-RAB1 Complex

The structure of Espg-RAB1 Complex, PDB code: 4fmc was solved by F.Shao, Y.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	107.566, 152.707, 226.706, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.7

The structure of Espg-RAB1 Complex also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	3 atoms

The binding sites of Magnesium atom in the Espg-RAB1 Complex (pdb code 4fmc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Espg-RAB1 Complex, PDB code: 4fmc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Espg-RAB1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Espg-RAB1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:52.6 occ:1.00 O B:HOH301 1.7 71.2 1.0 OG B:SER25 2.0 48.2 1.0 OG1 B:THR43 2.1 54.0 1.0 O3B B:GDP202 2.2 46.7 1.0 F2 B:AF3201 2.3 38.5 1.0 O B:HOH302 2.4 44.9 1.0 CB B:THR43 2.9 55.1 1.0 OD2 B:ASP66 3.2 55.9 1.0 OD1 B:ASP66 3.3 57.9 1.0 CB B:SER25 3.3 50.6 1.0 PB B:GDP202 3.6 48.6 1.0 CG B:ASP66 3.6 55.9 1.0 AL B:AF3201 3.7 39.1 1.0 CG2 B:THR43 3.8 54.8 1.0 N B:SER25 3.9 49.4 1.0 O1B B:GDP202 4.0 49.8 1.0 O B:THR67 4.0 52.1 1.0 CA B:SER25 4.1 50.4 1.0 CA B:THR43 4.1 56.6 1.0 N B:THR43 4.1 58.4 1.0 O2B B:GDP202 4.3 46.5 1.0 F1 B:AF3201 4.3 36.9 1.0 O A:HOH501 4.4 36.9 1.0 O1A B:GDP202 4.6 48.7 1.0 CB B:LYS24 4.7 47.8 1.0 O2A B:GDP202 4.7 45.4 1.0 C B:LYS24 4.8 49.0 1.0 O3A B:GDP202 4.9 47.9 1.0 CE B:LYS24 4.9 45.0 1.0 C B:THR67 4.9 52.2 1.0 PA B:GDP202 5.0 49.2 1.0 NZ B:LYS24 5.0 44.2 1.0

Magnesium binding site 2 out of 3 in the Espg-RAB1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Espg-RAB1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:78.1 occ:1.00 O1B D:GDP202 2.1 70.1 1.0 OG1 D:THR43 2.1 73.6 1.0 F2 D:AF3201 2.1 38.3 1.0 OG D:SER25 2.2 73.4 1.0 CB D:THR43 3.0 73.2 1.0 O D:HOH301 3.1 58.2 1.0 PB D:GDP202 3.3 72.3 1.0 AL D:AF3201 3.3 38.9 1.0 CB D:SER25 3.5 77.1 1.0 F1 D:AF3201 3.6 37.0 1.0 O D:THR67 3.6 67.1 1.0 OD1 D:ASP66 3.7 76.8 1.0 O3B D:GDP202 3.7 73.3 1.0 OD2 D:ASP66 3.7 77.1 1.0 CG2 D:THR43 3.8 72.3 1.0 O2B D:GDP202 3.8 70.0 1.0 N D:SER25 3.9 76.6 1.0 O C:HOH401 4.0 68.7 1.0 CG D:ASP66 4.1 75.5 1.0 CA D:SER25 4.2 77.6 1.0 CA D:THR43 4.3 74.2 1.0 NZ D:LYS24 4.3 64.2 1.0 N D:THR43 4.4 77.8 1.0 CE D:LYS24 4.5 65.1 1.0 O2A D:GDP202 4.5 79.1 1.0 C D:THR67 4.6 65.5 1.0 CB D:LYS24 4.6 72.0 1.0 O3A D:GDP202 4.7 77.7 1.0 C D:LYS24 4.9 76.2 1.0 O1A D:GDP202 4.9 80.1 1.0 F3 D:AF3201 5.0 38.2 1.0 PA D:GDP202 5.0 81.3 1.0

Magnesium binding site 3 out of 3 in the Espg-RAB1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Espg-RAB1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:0.8 occ:1.00 O3B F:GDP202 2.1 0.0 1.0 OG1 F:THR43 2.3 0.7 1.0 OG F:SER25 2.4 0.0 1.0 OD2 F:ASP66 2.5 0.0 1.0 F2 F:AF3201 2.8 34.6 1.0 OD1 F:ASP66 3.1 0.2 1.0 CG F:ASP66 3.2 0.8 1.0 PB F:GDP202 3.3 0.2 1.0 CB F:THR43 3.3 0.2 1.0 CB F:SER25 3.5 0.3 1.0 O2B F:GDP202 3.5 0.9 1.0 N F:SER25 3.6 1.0 1.0 AL F:AF3201 3.8 34.5 1.0 NZ F:LYS24 3.9 0.7 1.0 O F:THR67 4.0 0.1 1.0 CA F:SER25 4.0 0.5 1.0 CG2 F:THR43 4.0 0.3 1.0 O1B F:GDP202 4.1 0.6 1.0 CB F:LYS24 4.2 0.1 1.0 C F:LYS24 4.4 0.2 1.0 CE F:LYS24 4.6 0.1 1.0 O2A F:GDP202 4.6 0.2 1.0 CA F:THR43 4.6 0.9 1.0 O3A F:GDP202 4.7 0.5 1.0 CB F:ASP66 4.7 0.1 1.0 N F:THR43 4.7 0.8 1.0 CA F:LYS24 4.7 0.4 1.0 N F:LYS24 4.9 0.9 1.0 CG F:LYS24 4.9 0.2 1.0 C F:THR67 4.9 0.0 1.0

N.Dong, Y.Zhu, Q.Lu, L.Hu, Y.Zheng, F.Shao. Structurally Distinct Bacterial Tbc-Like Gaps Link Arf Gtpase to RAB1 Inactivation to Counteract Host Defenses. Cell(Cambridge,Mass.) V. 150 1029 2012.
ISSN: ISSN 0092-8674
PubMed: 22939626
DOI: 10.1016/J.CELL.2012.06.050