Magnesium in PDB 2wb4: Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp

All present enzymatic activity of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp:
2.7.7.65;

The structure of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp, PDB code: 2wb4 was solved by P.Wassmann, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.00 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	123.560, 127.430, 88.130, 90.00, 90.00, 90.00
R / Rfree (%)	23.906 / 26.816

The structure of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp (pdb code 2wb4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp, PDB code: 2wb4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.2 occ:1.00 OD1 A:ASP10 2.2 14.4 1.0 F2 A:BEF501 2.2 14.4 1.0 O A:MET55 2.2 11.9 1.0 OD2 A:ASP53 2.2 8.3 1.0 O A:HOH2002 2.5 4.0 1.0 CG A:ASP10 3.0 11.8 1.0 OD2 A:ASP10 3.3 11.2 1.0 C A:MET55 3.4 12.0 1.0 CG A:ASP53 3.4 11.6 1.0 BE A:BEF501 3.6 19.9 1.0 OD1 A:ASP53 4.0 15.5 1.0 CB A:MET55 4.1 12.3 1.0 CA A:MET55 4.2 11.7 1.0 OD1 A:ASP9 4.3 12.7 1.0 N A:MET56 4.4 11.7 1.0 CB A:ASP10 4.4 11.5 1.0 CG A:MET56 4.5 12.4 1.0 F1 A:BEF501 4.5 13.5 1.0 F3 A:BEF501 4.5 23.3 1.0 N A:MET55 4.5 11.2 1.0 CA A:MET56 4.6 12.0 1.0 N A:ASP10 4.6 10.7 1.0 CB A:ASP53 4.6 11.4 1.0 CD1 A:ILE11 4.8 13.4 1.0 CG1 A:ILE11 4.9 13.5 1.0 CG A:ASP9 5.0 14.2 1.0

Magnesium binding site 2 out of 3 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:12.7 occ:1.00 O B:HOH2001 1.8 4.6 1.0 O B:HOH2002 2.0 24.3 1.0 F2 B:BEF501 2.1 3.1 1.0 OD1 B:ASP10 2.2 14.7 1.0 OD2 B:ASP53 2.2 8.7 1.0 O B:MET55 2.2 10.8 1.0 CG B:ASP10 3.1 11.9 1.0 OD2 B:ASP10 3.3 10.6 1.0 CG B:ASP53 3.3 12.0 1.0 C B:MET55 3.4 11.8 1.0 BE B:BEF501 3.5 7.6 1.0 OD1 B:ASP53 3.9 15.2 1.0 CB B:MET55 4.2 12.4 1.0 CA B:MET55 4.2 11.5 1.0 OD1 B:ASP9 4.2 12.4 1.0 F1 B:BEF501 4.3 6.3 1.0 N B:MET56 4.3 11.6 1.0 F3 B:BEF501 4.4 5.7 1.0 CB B:ASP10 4.4 11.8 1.0 CG B:MET56 4.4 12.6 1.0 N B:MET55 4.5 10.9 1.0 CA B:MET56 4.6 11.7 1.0 N B:ASP10 4.6 10.9 1.0 CB B:ASP53 4.6 11.3 1.0 CD1 B:ILE11 4.8 13.4 1.0 CG1 B:ILE11 4.8 13.6 1.0 CG B:ASP9 4.9 14.3 1.0 CA B:ASP10 5.0 11.2 1.0

Magnesium binding site 3 out of 3 in the Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Activated Diguanylate Cyclase Pled in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg509 b:29.4 occ:1.00 OE2 B:GLU371 2.2 25.1 1.0 O11 B:C2E507 2.2 23.8 1.0 N B:GLU370 3.1 12.5 1.0 CD B:GLU371 3.2 16.8 1.0 CG B:GLU370 3.4 15.7 1.0 N B:GLY369 3.4 12.6 1.0 P11 B:C2E507 3.6 16.7 1.0 CG B:GLU371 3.8 14.8 1.0 CA B:GLY369 3.8 12.3 1.0 C B:GLY368 3.9 12.2 1.0 N B:GLU371 3.9 11.8 1.0 C B:GLY369 3.9 12.8 1.0 CA B:GLU370 3.9 12.2 1.0 O5A B:C2E507 4.0 17.8 1.0 C B:GLU370 4.1 12.1 1.0 C5A B:C2E507 4.1 19.1 1.0 CB B:GLU371 4.2 11.8 1.0 CB B:GLU370 4.2 12.2 1.0 CA B:GLY368 4.3 11.5 1.0 OE1 B:GLU371 4.3 21.6 1.0 O21 B:C2E507 4.3 8.3 1.0 CD B:GLU370 4.4 18.6 1.0 O B:GLY368 4.5 13.7 1.0 OE2 B:GLU370 4.7 17.9 1.0 CA B:GLU371 4.7 11.7 1.0 O3' B:C2E507 4.8 20.1 1.0 O B:GLU370 4.9 12.6 1.0

P.Wassmann, C.Massa, F.Zaehringer, T.Schirmer. Crystal Structure of Activated Pled, Identification of Dimerization and Catalysis Relevant Regulatory Mechanisms To Be Published.