Magnesium in PDB 7e1h: Crystal Structure of Rd-Bef

The structure of Crystal Structure of Rd-Bef, PDB code: 7e1h was solved by S.Hong, X.Zhang, P.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.81
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	130.858, 130.858, 271.355, 90, 90, 120
R / Rfree (%)	22.6 / 25.3

The structure of Crystal Structure of Rd-Bef also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Magnesium atom in the Crystal Structure of Rd-Bef (pdb code 7e1h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Rd-Bef, PDB code: 7e1h:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Rd-Bef


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 Rd-Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:13.8 occ:1.00 F1 A:BEF201 1.9 35.1 1.0 OD1 A:ASP10 2.0 30.2 1.0 OD2 A:ASP51 2.2 19.8 1.0 BE A:BEF201 2.7 28.4 1.0 CG A:ASP10 2.7 31.8 1.0 O A:GLN53 2.8 49.7 1.0 OD2 A:ASP10 2.8 29.8 1.0 CG A:ASP51 2.9 25.4 1.0 OD1 A:ASP51 3.1 36.3 1.0 OE2 A:GLU9 3.5 34.7 1.0 F2 A:BEF201 3.6 18.8 1.0 C A:GLN53 3.8 44.7 1.0 F3 A:BEF201 3.8 23.7 1.0 OD1 I:ASP96 3.9 32.4 1.0 OD2 I:ASP96 3.9 28.8 1.0 CB A:ASP10 4.1 30.8 1.0 CB A:ASP51 4.3 20.1 1.0 CG I:ASP96 4.3 32.0 1.0 N A:ASP10 4.4 25.9 1.0 N A:GLN53 4.5 24.6 1.0 CA A:GLN53 4.6 28.0 1.0 N A:LEU54 4.6 36.7 1.0 N A:ASP11 4.7 32.4 1.0 NZ A:LYS100 4.7 22.1 1.0 CD A:GLU9 4.7 35.2 1.0 CA A:ASP10 4.7 21.5 1.0 CB A:GLN53 4.8 33.6 1.0 O I:HOH223 4.8 39.2 1.0 CA A:LEU54 4.9 29.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Rd-Bef


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 Rd-Bef within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:14.7 occ:1.00 F1 B:BEF201 2.0 26.4 1.0 O B:GLN53 2.1 18.8 1.0 OD2 B:ASP10 2.2 23.3 1.0 OE1 B:GLU9 2.2 22.5 1.0 O B:HOH319 2.4 30.5 1.0 CD2 B:LEU54 2.8 22.9 1.0 CD B:GLU9 3.0 27.7 1.0 OE2 B:GLU9 3.1 27.2 1.0 CG B:ASP10 3.2 24.6 1.0 C B:GLN53 3.2 14.0 1.0 BE B:BEF201 3.3 18.5 1.0 OD1 B:ASP10 3.5 30.8 1.0 CG B:ASP51 3.7 25.6 1.0 OD1 B:ASP51 3.8 26.3 1.0 OD2 B:ASP51 3.9 22.1 1.0 CA B:LEU54 4.0 22.8 1.0 N B:LEU54 4.0 18.6 1.0 CB B:ASP51 4.1 20.4 1.0 CG B:LEU54 4.2 23.9 1.0 N B:ASP10 4.2 22.4 1.0 F2 B:BEF201 4.2 13.1 1.0 CA B:GLN53 4.3 14.3 1.0 F3 B:BEF201 4.3 26.0 1.0 N B:GLN53 4.4 9.7 1.0 CG B:GLU9 4.5 30.3 1.0 CB B:ASP10 4.6 22.1 1.0 CB B:LEU54 4.6 24.7 1.0 CB B:GLN53 4.7 12.9 1.0 O J:HOH214 4.7 26.0 1.0 CA B:GLU9 4.8 20.3 1.0 CE1 J:TYR97 4.9 16.8 1.0 O J:HOH227 4.9 13.7 1.0 CB B:GLU9 5.0 20.0 1.0 CA B:ASP10 5.0 20.0 1.0 OE1 B:GLN53 5.0 16.4 1.0 OH J:TYR97 5.0 31.3 1.0 N B:ARG52 5.0 9.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Rd-Bef


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 Rd-Bef within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:30.7 occ:1.00 O E:GLN53 1.9 23.5 1.0 OD1 E:ASP10 2.0 34.5 1.0 OD2 E:ASP10 2.1 34.3 1.0 CG E:ASP10 2.2 36.9 1.0 F1 E:BEF201 2.3 31.5 1.0 OD2 E:ASP51 2.8 42.2 1.0 C E:GLN53 3.1 28.1 1.0 BE E:BEF201 3.4 30.1 1.0 CB E:ASP10 3.6 35.7 1.0 CA E:LEU54 3.8 36.8 1.0 N E:LEU54 3.8 26.8 1.0 CG E:ASP51 4.0 47.1 1.0 OE1 E:GLN53 4.1 28.1 1.0 OE2 E:GLU9 4.1 38.6 1.0 F2 E:BEF201 4.2 18.2 1.0 CA E:GLN53 4.2 37.8 1.0 N E:ASP10 4.4 46.1 1.0 CB E:GLN53 4.4 31.4 1.0 CG E:LEU54 4.4 36.5 1.0 CA E:ASP10 4.6 36.3 1.0 F3 E:BEF201 4.7 29.5 1.0 OD1 E:ASP51 4.7 46.9 1.0 N E:GLN53 4.7 44.4 1.0 CB E:LEU54 4.7 38.6 1.0 N E:ASP11 4.8 37.0 1.0 C E:LEU54 4.9 37.8 1.0 CD E:GLU9 4.9 43.0 1.0 CD1 E:LEU54 5.0 35.7 1.0 CD E:GLN53 5.0 37.6 1.0

S.Hong, P.Zhang. Structural Basis of Phosphorylation-Induced Activation of the Response Regulator Vbrr To Be Published.