Magnesium in PDB 7dn9: Crystal Structure of Salmonella Effector in Complex with Nad and Host Co-Factor ARF1

The structure of Crystal Structure of Salmonella Effector in Complex with Nad and Host Co-Factor ARF1, PDB code: 7dn9 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)	46.91 / 3.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.711, 105.576, 105.839, 90, 104.8, 90
R / Rfree (%)	23.6 / 27.7

The binding sites of Magnesium atom in the Crystal Structure of Salmonella Effector in Complex with Nad and Host Co-Factor ARF1 (pdb code 7dn9). 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 in Complex with Nad and Host Co-Factor ARF1, PDB code: 7dn9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Salmonella Effector in Complex with Nad and Host Co-Factor 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 in Complex with Nad and Host Co-Factor ARF1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:42.4 occ:1.00 O1B B:GDP202 2.3 37.9 1.0 OG1 B:THR48 2.9 59.6 1.0 O3B B:GDP202 3.0 35.7 1.0 PB B:GDP202 3.2 30.3 1.0 CB B:THR48 3.5 57.1 1.0 NZ B:LYS30 3.6 39.4 1.0 OG1 B:THR31 3.8 34.3 1.0 N B:THR48 3.9 46.5 1.0 O2B B:GDP202 4.0 35.6 1.0 O2A B:GDP202 4.1 51.4 1.0 CA B:THR48 4.3 57.5 1.0 O3A B:GDP202 4.5 35.4 1.0 CG2 B:THR48 4.7 47.6 1.0 O B:ILE46 4.8 58.5 1.0 PA B:GDP202 4.9 36.2 1.0 CA B:GLY69 4.9 57.4 1.0 O B:GLY69 4.9 70.9 1.0 CB B:THR31 5.0 37.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Salmonella Effector in Complex with Nad and Host Co-Factor 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 in Complex with Nad and Host Co-Factor ARF1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:48.8 occ:1.00 O1B D:GDP202 2.3 48.0 1.0 OG1 D:THR48 3.1 62.4 1.0 PB D:GDP202 3.3 36.8 1.0 O3B D:GDP202 3.4 37.1 1.0 CB D:THR48 3.5 60.5 1.0 NZ D:LYS30 3.6 58.3 1.0 N D:THR48 3.9 52.6 1.0 O2B D:GDP202 4.0 39.8 1.0 OG1 D:THR31 4.2 42.0 1.0 CA D:THR48 4.3 52.7 1.0 O2A D:GDP202 4.4 49.8 1.0 O D:GLY69 4.6 73.9 1.0 CA D:GLY69 4.7 66.0 1.0 O3A D:GDP202 4.7 43.1 1.0 CG2 D:THR48 4.8 56.8 1.0 CB D:ASP26 4.9 57.5 1.0 O D:THR48 5.0 51.2 1.0 O D:ILE46 5.0 67.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Salmonella Effector in Complex with Nad and Host Co-Factor 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 in Complex with Nad and Host Co-Factor ARF1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:40.1 occ:1.00 O1B F:GDP202 2.4 44.0 1.0 OG1 F:THR48 3.0 55.6 1.0 O3B F:GDP202 3.4 41.6 1.0 PB F:GDP202 3.5 35.3 1.0 CB F:THR48 3.5 51.8 1.0 NZ F:LYS30 3.8 45.6 1.0 N F:THR48 3.8 46.0 1.0 OG1 F:THR31 4.2 35.5 1.0 O2B F:GDP202 4.2 34.5 1.0 CA F:THR48 4.3 44.8 1.0 O2A F:GDP202 4.3 42.1 1.0 O F:GLY69 4.6 80.9 1.0 CA F:GLY69 4.7 73.5 1.0 CG2 F:THR48 4.7 51.8 1.0 O3A F:GDP202 4.8 39.9 1.0 O F:ILE46 4.8 67.4 1.0 C F:PRO47 4.9 56.7 1.0 O F:THR48 5.0 51.0 1.0 CB F:ASP26 5.0 53.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Salmonella Effector in Complex with Nad and Host Co-Factor 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 in Complex with Nad and Host Co-Factor ARF1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg201 b:46.1 occ:1.00 O1B H:GDP202 2.2 37.8 1.0 OG1 H:THR48 2.7 62.4 1.0 O3B H:GDP202 2.8 40.9 1.0 PB H:GDP202 3.0 34.0 1.0 OG1 H:THR31 3.4 40.4 1.0 CB H:THR48 3.5 59.2 1.0 O2A H:GDP202 3.8 46.1 1.0 NZ H:LYS30 3.8 51.3 1.0 O2B H:GDP202 3.9 35.2 1.0 N H:THR48 4.0 57.3 1.0 O3A H:GDP202 4.2 40.6 1.0 CA H:THR48 4.4 60.0 1.0 CB H:THR31 4.5 42.6 1.0 O H:ILE46 4.5 67.1 1.0 PA H:GDP202 4.5 35.6 1.0 CG2 H:THR48 4.7 48.9 1.0 N H:THR31 5.0 40.9 1.0

J.Ding, Y.Xu, F.Shao. Crystal Structure of Salmonella Effector in Complex with Nad and Host Co-Factor ARF1 To Be Published.