Magnesium in PDB 4fmd: Espg-RAB1 Complex Structure at 3.05 A

The structure of Espg-RAB1 Complex Structure at 3.05 A, PDB code: 4fmd 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 / 3.05
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.568, 153.221, 230.805, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.6

The structure of Espg-RAB1 Complex Structure at 3.05 A also contains other interesting chemical elements:

Fluorine	(F)	9 atoms
Aluminium	(Al)	3 atoms

The binding sites of Magnesium atom in the Espg-RAB1 Complex Structure at 3.05 A (pdb code 4fmd). 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 Structure at 3.05 A, PDB code: 4fmd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:53.1 occ:1.00 O3B B:GDP202 1.9 61.2 1.0 F2 B:AF3201 2.0 50.4 1.0 OG B:SER25 2.1 64.2 1.0 O B:HOH301 2.1 41.1 1.0 OG1 B:THR43 2.3 68.0 1.0 O B:HOH302 2.3 81.7 1.0 CB B:THR43 2.8 68.7 1.0 PB B:GDP202 3.2 61.5 1.0 CB B:SER25 3.3 65.0 1.0 AL B:AF3201 3.4 49.6 1.0 O2B B:GDP202 3.5 66.0 1.0 N B:THR43 3.8 72.2 1.0 CG2 B:THR43 3.9 68.3 1.0 CA B:THR43 3.9 70.4 1.0 OD2 B:ASP66 4.0 63.3 1.0 O1B B:GDP202 4.0 57.6 1.0 N B:SER25 4.0 63.7 1.0 F1 B:AF3201 4.1 48.9 1.0 OD1 B:ASP66 4.2 62.5 1.0 O1A B:GDP202 4.2 61.7 1.0 CA B:SER25 4.2 64.3 1.0 O A:HOH401 4.2 49.5 1.0 O3A B:GDP202 4.4 62.9 1.0 CG B:ASP66 4.5 62.0 1.0 O2A B:GDP202 4.5 61.6 1.0 PA B:GDP202 4.6 61.8 1.0 O B:THR67 4.6 61.1 1.0 NH2 A:ARG208 4.7 70.6 1.0 F3 B:AF3201 4.8 49.2 1.0 C B:SER42 4.9 75.1 1.0

Magnesium binding site 2 out of 3 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:69.4 occ:1.00 O D:HOH301 1.8 75.7 1.0 O1B D:GDP202 1.8 78.8 1.0 F2 D:AF3201 2.0 51.2 1.0 O D:HOH302 2.3 76.2 1.0 OG D:SER25 2.4 79.5 1.0 OG1 D:THR43 2.8 81.7 1.0 PB D:GDP202 3.0 80.7 1.0 CB D:THR43 3.0 80.2 1.0 AL D:AF3201 3.1 51.7 1.0 O3B D:GDP202 3.1 82.6 1.0 CB D:SER25 3.5 82.3 1.0 F1 D:AF3201 3.6 51.0 1.0 OD2 D:ASP66 3.8 77.9 1.0 O2B D:GDP202 3.8 79.3 1.0 N D:THR43 3.9 83.5 1.0 CG2 D:THR43 4.0 79.3 1.0 N D:SER25 4.1 82.4 1.0 CA D:THR43 4.1 80.9 1.0 O2A D:GDP202 4.1 83.6 1.0 O C:HOH501 4.1 51.2 1.0 O3A D:GDP202 4.3 84.3 1.0 O D:THR67 4.3 71.6 1.0 OD1 D:ASP66 4.3 78.1 1.0 CA D:SER25 4.4 82.7 1.0 CG D:ASP66 4.4 76.6 1.0 PA D:GDP202 4.5 86.0 1.0 O1A D:GDP202 4.5 84.2 1.0 NH2 C:ARG208 4.6 88.6 1.0 F3 D:AF3201 4.6 50.8 1.0 CB D:LYS24 4.9 80.5 1.0 C D:LYS24 5.0 82.5 1.0

Magnesium binding site 3 out of 3 in the Espg-RAB1 Complex Structure at 3.05 A


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 Structure at 3.05 A within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:91.3 occ:1.00 OG F:SER25 1.9 0.7 1.0 O3B F:GDP202 1.9 0.4 1.0 OG1 F:THR43 2.0 0.8 1.0 F2 F:AF3201 2.2 62.5 1.0 O F:HOH301 2.6 92.6 1.0 CB F:THR43 3.0 0.9 1.0 CB F:SER25 3.2 0.4 1.0 PB F:GDP202 3.3 0.0 1.0 AL F:AF3201 3.6 62.5 1.0 O2A F:GDP202 3.6 0.4 1.0 O1B F:GDP202 3.6 0.3 1.0 OD2 F:ASP66 3.7 0.7 1.0 N F:THR43 3.8 0.8 1.0 CA F:THR43 4.0 0.2 1.0 N F:SER25 4.0 0.2 1.0 CG2 F:THR43 4.1 0.4 1.0 CA F:SER25 4.1 0.1 1.0 O2B F:GDP202 4.3 0.3 1.0 F1 F:AF3201 4.3 62.4 1.0 O3A F:GDP202 4.4 0.9 1.0 OD1 F:ASP66 4.4 0.4 1.0 CG F:ASP66 4.5 0.5 1.0 PA F:GDP202 4.5 0.7 1.0 O E:HOH501 4.7 62.4 1.0 O1A F:GDP202 4.8 0.6 1.0 C F:SER42 4.8 0.4 1.0 O F:THR67 4.8 1.0 1.0 NH2 E:ARG208 4.9 0.8 1.0 F3 F:AF3201 5.0 62.4 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