Magnesium in PDB 7dn8: Crystal Structure of Salmonella Effector Sopf in Complex with ARF1

The structure of Crystal Structure of Salmonella Effector Sopf in Complex with ARF1, PDB code: 7dn8 was solved by J.Ding, F.Shao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.65 / 2.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.737, 104.902, 105.603, 90, 104.88, 90
R / Rfree (%)	20.1 / 24

The binding sites of Magnesium atom in the Crystal Structure of Salmonella Effector Sopf in Complex with ARF1 (pdb code 7dn8). 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 Salmonella Effector Sopf in Complex with ARF1, PDB code: 7dn8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Salmonella Effector Sopf in Complex with ARF1


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 Salmonella Effector Sopf in Complex with ARF1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:34.4 occ:1.00 O D:HOH307 2.0 35.5 1.0 O2B D:GDP202 2.1 32.0 1.0 O D:HOH319 2.1 33.4 1.0 O D:HOH304 2.1 34.3 1.0 OG1 D:THR48 2.3 33.2 1.0 OG1 D:THR31 2.4 31.5 1.0 O3B D:GDP202 3.1 34.0 1.0 PB D:GDP202 3.1 29.9 1.0 CB D:THR48 3.3 38.5 1.0 CB D:THR31 3.6 36.3 1.0 NZ D:LYS30 3.6 49.6 1.0 OD2 D:ASP67 3.9 31.2 1.0 O1B D:GDP202 4.0 33.4 1.0 O2A D:GDP202 4.0 37.0 1.0 N D:THR31 4.0 34.3 1.0 O D:HOH306 4.1 35.9 1.0 CG2 D:THR48 4.2 34.2 1.0 OD1 D:ASP67 4.2 33.7 1.0 O3A D:GDP202 4.3 33.2 1.0 O D:HOH311 4.3 38.6 1.0 CA D:THR31 4.4 32.6 1.0 N D:THR48 4.5 44.1 1.0 CG D:ASP67 4.5 26.9 1.0 CA D:THR48 4.5 41.3 1.0 PA D:GDP202 4.6 32.8 1.0 CG2 D:THR31 4.6 32.0 1.0 O1A D:GDP202 4.7 29.5 1.0 O D:ILE46 4.7 46.2 1.0 CB D:LYS30 4.9 27.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Salmonella Effector Sopf in Complex with ARF1


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 Salmonella Effector Sopf in Complex with ARF1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:31.8 occ:1.00 O3B B:GDP202 2.1 34.8 1.0 O B:HOH302 2.2 30.1 1.0 O B:HOH318 2.3 29.7 1.0 OG1 B:THR48 2.3 35.7 1.0 OG1 B:THR31 2.5 30.4 1.0 PB B:GDP202 3.1 29.4 1.0 O1B B:GDP202 3.2 27.9 1.0 NZ B:LYS30 3.2 48.9 1.0 CB B:THR48 3.3 38.8 1.0 OD2 B:ASP67 3.7 29.4 1.0 CB B:THR31 3.8 35.8 1.0 O2B B:GDP202 3.9 31.2 1.0 OD1 B:ASP67 3.9 37.8 1.0 CG2 B:THR48 4.0 38.1 1.0 N B:THR31 4.1 33.4 1.0 CG B:ASP67 4.2 31.3 1.0 O1A B:GDP202 4.5 30.9 1.0 O3A B:GDP202 4.5 32.1 1.0 CA B:THR31 4.5 35.5 1.0 CA B:THR48 4.5 44.2 1.0 O B:HOH312 4.6 34.0 1.0 N B:THR48 4.6 43.1 1.0 CB B:LYS30 4.7 34.2 1.0 CE B:LYS30 4.7 32.5 1.0 CG2 B:THR31 4.9 32.6 1.0 PA B:GDP202 4.9 32.2 1.0 CA B:GLY69 4.9 50.6 1.0 O2A B:GDP202 4.9 28.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Salmonella Effector Sopf in Complex with ARF1


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 Salmonella Effector Sopf in Complex with ARF1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:30.3 occ:1.00 OG1 F:THR48 2.1 29.0 1.0 O F:HOH311 2.1 32.8 1.0 O2B F:GDP202 2.2 37.1 1.0 OG1 F:THR31 2.2 23.9 1.0 O F:HOH302 2.3 21.9 1.0 O F:HOH313 2.3 26.8 1.0 CB F:THR48 3.2 37.2 1.0 PB F:GDP202 3.3 39.0 1.0 O3B F:GDP202 3.3 30.9 1.0 CB F:THR31 3.4 31.3 1.0 OD2 F:ASP67 3.7 30.2 1.0 CG2 F:THR48 3.9 34.7 1.0 OD1 F:ASP67 4.0 31.6 1.0 N F:THR31 4.1 31.1 1.0 O F:HOH315 4.1 34.5 1.0 O2A F:GDP202 4.2 33.5 1.0 O1B F:GDP202 4.2 26.6 1.0 CG F:ASP67 4.3 26.7 1.0 CA F:THR31 4.3 31.2 1.0 CA F:THR48 4.4 40.1 1.0 N F:THR48 4.4 41.9 1.0 CG2 F:THR31 4.5 26.7 1.0 O3A F:GDP202 4.5 28.3 1.0 PA F:GDP202 4.7 32.8 1.0 O F:ILE46 4.7 44.5 1.0 O1A F:GDP202 4.8 28.8 1.0 CB F:LYS30 4.9 28.0 1.0 CE F:LYS30 4.9 28.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Salmonella Effector Sopf in Complex with ARF1


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 Salmonella Effector Sopf in Complex with ARF1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg201 b:32.1 occ:1.00 O H:HOH302 2.1 27.6 1.0 O3B H:GDP202 2.1 32.5 1.0 O H:HOH321 2.2 27.9 1.0 OG1 H:THR48 2.3 33.7 1.0 OG1 H:THR31 2.4 28.5 1.0 O H:HOH304 2.4 34.3 1.0 O1B H:GDP202 3.0 25.9 1.0 PB H:GDP202 3.1 25.9 1.0 CB H:THR48 3.3 35.7 1.0 CB H:THR31 3.5 33.5 1.0 OD2 H:ASP67 3.9 30.0 1.0 O1A H:GDP202 4.0 33.5 1.0 O2B H:GDP202 4.1 28.2 1.0 N H:THR31 4.1 32.3 1.0 CG2 H:THR48 4.2 34.2 1.0 O H:HOH307 4.2 36.2 1.0 OD1 H:ASP67 4.3 31.5 1.0 O3A H:GDP202 4.3 28.6 1.0 CA H:THR31 4.4 27.0 1.0 N H:THR48 4.4 45.7 1.0 CA H:THR48 4.5 42.2 1.0 PA H:GDP202 4.5 31.0 1.0 CG H:ASP67 4.6 30.7 1.0 CG2 H:THR31 4.6 26.3 1.0 O2A H:GDP202 4.7 27.1 1.0 O H:ILE46 4.7 46.5 1.0 CE H:LYS30 4.9 26.2 1.0 CB H:LYS30 4.9 24.7 1.0

Y.Xu, J.Ding, F.Shao. Crystal Structure of Salmonella Effector Sopf in Complex with ARF1 To Be Published.