Magnesium in PDB 3qyy: A Novel Interaction Mode Between A Microbial Ggdef Domain and the Bis- (3, 5 )-Cyclic Di-Gmp

The structure of A Novel Interaction Mode Between A Microbial Ggdef Domain and the Bis- (3, 5 )-Cyclic Di-Gmp, PDB code: 3qyy was solved by C.-Y.Yang, K.-H.Chin, S.-H.Chou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.281, 87.281, 87.860, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.9

The binding sites of Magnesium atom in the A Novel Interaction Mode Between A Microbial Ggdef Domain and the Bis- (3, 5 )-Cyclic Di-Gmp (pdb code 3qyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A Novel Interaction Mode Between A Microbial Ggdef Domain and the Bis- (3, 5 )-Cyclic Di-Gmp, PDB code: 3qyy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the A Novel Interaction Mode Between A Microbial Ggdef Domain and the Bis- (3, 5 )-Cyclic Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Novel Interaction Mode Between A Microbial Ggdef Domain and the Bis- (3, 5 )-Cyclic Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:15.0 occ:1.00 O11 A:C2E487 2.0 13.3 1.0 OD1 A:ASP216 2.0 12.5 1.0 OD1 A:ASP173 2.0 13.1 1.0 O A:HOH381 2.1 12.3 1.0 O A:HOH383 2.1 14.8 1.0 O A:HOH382 2.2 14.5 1.0 CG A:ASP216 3.0 16.1 1.0 CG A:ASP173 3.0 17.1 1.0 O A:HOH323 3.3 15.0 1.0 OD2 A:ASP216 3.3 17.9 1.0 OD2 A:ASP173 3.3 17.7 1.0 P11 A:C2E487 3.4 13.0 1.0 O21 A:C2E487 3.9 12.6 1.0 O2' B:C2E486 4.1 14.3 1.0 O5A A:C2E487 4.2 12.9 1.0 OE2 A:GLU217 4.3 16.9 1.0 CB A:ASP216 4.4 14.0 1.0 CB A:ASP173 4.4 12.8 1.0 C A:ASP216 4.4 13.6 1.0 O B:HOH359 4.4 20.9 1.0 O3' A:C2E487 4.4 15.2 1.0 O A:MET174 4.4 14.4 1.0 O A:ASP216 4.5 14.3 1.0 C5A A:C2E487 4.6 13.4 1.0 N A:ASP216 4.6 14.7 1.0 O A:HOH464 4.7 17.9 1.0 CB A:GLU217 4.7 12.8 1.0 N A:GLU217 4.7 12.7 1.0 CA A:ASP216 4.7 14.1 1.0 O A:HOH357 4.7 18.8 1.0 N A:MET174 4.8 14.3 1.0 CA A:ASP173 4.9 12.7 1.0 O A:HOH358 5.0 28.1 1.0 O A:HOH437 5.0 27.4 1.0

Magnesium binding site 2 out of 2 in the A Novel Interaction Mode Between A Microbial Ggdef Domain and the Bis- (3, 5 )-Cyclic Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Novel Interaction Mode Between A Microbial Ggdef Domain and the Bis- (3, 5 )-Cyclic Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:15.2 occ:1.00 O11 B:C2E486 2.0 14.8 1.0 O B:HOH379 2.0 14.2 1.0 OD2 B:ASP173 2.0 14.9 1.0 OD2 B:ASP216 2.1 16.2 1.0 O B:HOH380 2.2 13.5 1.0 O B:HOH378 2.2 15.7 1.0 CG B:ASP173 3.0 18.6 1.0 CG B:ASP216 3.0 15.7 1.0 O B:HOH362 3.2 12.7 1.0 OD1 B:ASP173 3.2 19.9 1.0 OD1 B:ASP216 3.3 17.2 1.0 P11 B:C2E486 3.4 13.8 1.0 O21 B:C2E486 3.9 12.9 1.0 O2' A:C2E487 4.2 12.6 1.0 O5A B:C2E486 4.2 14.2 1.0 OE1 B:GLU217 4.3 17.4 1.0 O3' B:C2E486 4.4 14.7 1.0 O A:HOH464 4.4 17.9 1.0 CB B:ASP173 4.4 16.2 1.0 CB B:ASP216 4.4 16.5 1.0 O B:MET174 4.4 16.9 1.0 C B:ASP216 4.4 14.9 1.0 O B:ASP216 4.5 15.2 1.0 C5A B:C2E486 4.6 13.4 1.0 O B:HOH359 4.6 20.9 1.0 N B:ASP216 4.6 14.8 1.0 N B:GLU217 4.7 14.4 1.0 CA B:ASP216 4.7 15.1 1.0 N B:MET174 4.8 17.0 1.0 CB B:GLU217 4.8 15.3 1.0 O B:HOH372 4.9 23.8 1.0 CA B:ASP173 4.9 17.2 1.0 O B:HOH321 5.0 21.0 1.0

C.-Y.Yang, K.-H.Chin, M.L.-C.Chuah, Z.-X.Liang, A.H.-J.Wang, S.-H.Chou. The Structure and Inhibition of A Ggdef Diguanylate Cyclase Complexed with (C-Di-Gmp)(2) at the Active Site Acta Crystallogr.,Sect.D V. 67 997 2011.
ISSN: ISSN 0907-4449
PubMed: 22120736
DOI: 10.1107/S090744491104039X