Magnesium in PDB 4fme: Espg-RAB1-ARF6 Complex

The structure of Espg-RAB1-ARF6 Complex, PDB code: 4fme 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 / 4.10
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	137.222, 137.222, 126.503, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.9

The structure of Espg-RAB1-ARF6 Complex also contains other interesting chemical elements:

Aluminium	(Al)	2 atoms
Fluorine	(F)	6 atoms

The binding sites of Magnesium atom in the Espg-RAB1-ARF6 Complex (pdb code 4fme). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Espg-RAB1-ARF6 Complex, PDB code: 4fme:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Espg-RAB1-ARF6 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-ARF6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:85.5 occ:1.00 O B:HOH301 2.4 88.5 1.0 OG1 B:THR43 2.6 0.7 1.0 OG B:SER25 2.7 1.0 1.0 F2 B:AF3201 2.8 0.2 1.0 OD2 B:ASP66 2.9 0.0 1.0 CB B:THR43 3.0 0.7 1.0 O3B B:GDP202 3.0 0.4 1.0 F1 B:AF3201 3.4 0.9 1.0 O1B B:GDP202 3.4 0.6 1.0 AL B:AF3201 3.5 0.0 1.0 CG B:ASP66 3.7 0.0 1.0 CB B:SER25 3.8 1.0 1.0 PB B:GDP202 3.8 0.9 1.0 CG2 B:THR43 3.9 0.7 1.0 OD1 B:ASP66 4.0 0.0 1.0 CA B:THR43 4.2 0.6 1.0 N B:THR43 4.2 0.6 1.0 N B:SER25 4.4 0.6 1.0 O1A B:GDP202 4.4 0.0 1.0 O A:HOH401 4.5 0.8 1.0 CA B:SER25 4.5 0.6 1.0 O B:THR67 4.5 0.9 1.0 O2B B:GDP202 4.7 1.0 1.0 CB B:LYS24 4.9 0.8 1.0 C B:LYS24 5.0 0.5 1.0

Magnesium binding site 2 out of 4 in the Espg-RAB1-ARF6 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-ARF6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:54.1 occ:1.00 OG1 C:THR27 2.5 79.3 1.0 OG1 C:THR44 2.5 0.7 1.0 O2B C:GTP201 2.6 0.8 1.0 O3B C:GTP201 2.6 0.6 1.0 O3G C:GTP201 2.7 0.8 1.0 O2G C:GTP201 2.9 0.6 1.0 PG C:GTP201 2.9 0.4 1.0 CB C:THR44 3.0 0.7 1.0 PB C:GTP201 3.1 0.4 1.0 CB C:THR27 3.4 79.3 1.0 O2A C:GTP201 3.6 84.6 1.0 N C:THR44 3.6 0.1 1.0 OD2 C:ASP63 3.7 0.8 1.0 CA C:THR44 3.9 0.1 1.0 N C:THR27 4.0 0.3 1.0 O3A C:GTP201 4.0 0.1 1.0 PA C:GTP201 4.1 0.3 1.0 O1A C:GTP201 4.2 0.1 1.0 CG2 C:THR44 4.2 0.7 1.0 CA C:THR27 4.3 0.3 1.0 OD1 C:ASP63 4.3 0.8 1.0 O C:ILE42 4.3 0.6 1.0 O1B C:GTP201 4.3 0.3 1.0 O1G C:GTP201 4.3 0.5 1.0 CG C:ASP63 4.4 0.8 1.0 CG2 C:THR27 4.5 79.3 1.0 OG1 C:THR41 4.5 0.8 1.0 C C:PRO43 4.8 0.1 1.0 CB C:LYS26 5.0 0.9 1.0

Magnesium binding site 3 out of 4 in the Espg-RAB1-ARF6 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-ARF6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg203 b:91.4 occ:1.00 O E:HOH301 2.4 87.0 1.0 OG E:SER25 2.6 0.1 1.0 OG1 E:THR43 2.7 0.9 1.0 OD2 E:ASP66 2.8 0.4 1.0 F2 E:AF3201 2.8 0.9 1.0 O3B E:GDP202 2.9 0.3 1.0 CB E:THR43 3.1 0.9 1.0 O1B E:GDP202 3.4 1.0 1.0 F1 E:AF3201 3.4 0.1 1.0 AL E:AF3201 3.5 1.0 1.0 CB E:SER25 3.7 0.1 1.0 CG E:ASP66 3.7 0.4 1.0 PB E:GDP202 3.8 1.0 1.0 OD1 E:ASP66 3.9 0.4 1.0 CG2 E:THR43 4.0 0.9 1.0 N E:SER25 4.1 0.5 1.0 N E:THR43 4.3 0.4 1.0 CA E:THR43 4.3 0.4 1.0 O1A E:GDP202 4.3 0.3 1.0 CA E:SER25 4.4 0.5 1.0 O D:HOH401 4.6 0.4 1.0 O E:THR67 4.6 0.3 1.0 O2B E:GDP202 4.7 0.9 1.0 CB E:LYS24 4.7 0.8 1.0 C E:LYS24 4.9 0.8 1.0

Magnesium binding site 4 out of 4 in the Espg-RAB1-ARF6 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Espg-RAB1-ARF6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:40.2 occ:1.00 O2B F:GTP201 2.5 0.9 1.0 OG1 F:THR27 2.5 74.8 1.0 O3B F:GTP201 2.5 0.5 1.0 OG1 F:THR44 2.6 0.3 1.0 O3G F:GTP201 2.7 0.5 1.0 O2G F:GTP201 2.9 0.8 1.0 PG F:GTP201 2.9 0.5 1.0 PB F:GTP201 3.1 0.9 1.0 CB F:THR44 3.1 0.3 1.0 CB F:THR27 3.4 74.8 1.0 O2A F:GTP201 3.4 83.2 1.0 N F:THR44 3.7 0.1 1.0 OD2 F:ASP63 3.8 1.0 1.0 N F:THR27 3.9 0.6 1.0 PA F:GTP201 4.0 99.2 1.0 O3A F:GTP201 4.0 0.3 1.0 CA F:THR44 4.0 0.1 1.0 O1A F:GTP201 4.1 0.7 1.0 CA F:THR27 4.3 0.6 1.0 O F:ILE42 4.3 0.7 1.0 O1B F:GTP201 4.3 0.1 1.0 CG2 F:THR44 4.3 0.3 1.0 O1G F:GTP201 4.3 0.9 1.0 OD1 F:ASP63 4.4 1.0 1.0 OG1 F:THR41 4.5 0.9 1.0 CG F:ASP63 4.5 1.0 1.0 CG2 F:THR27 4.5 74.8 1.0 C F:PRO43 4.8 0.7 1.0 CB F:LYS26 4.9 0.1 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