Magnesium in PDB 2v0n: Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S

The structure of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S, PDB code: 2v0n 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)	30.00 / 2.71
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.965, 132.557, 88.425, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.2

The structure of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S (pdb code 2v0n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S, PDB code: 2v0n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.2 occ:1.00 O A:HOH2001 1.9 25.7 1.0 F2 A:BEF501 2.2 35.4 1.0 OD1 A:ASP10 2.2 40.8 1.0 O A:MET55 2.2 38.6 1.0 OD2 A:ASP53 2.2 33.2 1.0 OD2 A:ASP10 2.7 38.9 1.0 CG A:ASP10 2.8 40.2 1.0 CG A:ASP53 3.4 37.4 1.0 C A:MET55 3.4 40.3 1.0 BE A:BEF501 3.5 39.4 1.0 OD1 A:ASP53 4.0 40.6 1.0 CB A:MET55 4.2 41.5 1.0 CA A:MET55 4.2 41.5 1.0 CB A:ASP10 4.3 38.0 1.0 OD1 A:ASP9 4.4 47.9 1.0 N A:MET56 4.4 40.6 1.0 F3 A:BEF501 4.4 35.3 1.0 F1 A:BEF501 4.4 39.1 1.0 CG A:MET56 4.5 42.7 1.0 N A:MET55 4.6 41.2 1.0 CB A:ASP53 4.6 39.6 1.0 N A:ASP10 4.6 38.2 1.0 CA A:MET56 4.6 41.9 1.0 CG A:ASP9 4.9 42.7 1.0 OD2 A:ASP9 4.9 45.6 1.0 CA A:ASP10 5.0 38.9 1.0 CG1 A:ILE11 5.0 40.9 1.0

Magnesium binding site 2 out of 5 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:45.4 occ:1.00 OE1 A:GLU370 2.2 48.2 1.0 O3G A:GAV600 2.2 48.7 1.0 OD1 A:ASP327 2.2 47.3 1.0 O2B A:GAV600 2.2 56.8 1.0 O A:ILE328 2.2 42.2 1.0 OE2 A:GLU370 2.5 48.1 1.0 CD A:GLU370 2.6 46.5 1.0 PB A:GAV600 3.0 51.4 1.0 O3B A:GAV600 3.0 51.8 1.0 PG A:GAV600 3.0 49.4 1.0 CG A:ASP327 3.1 42.8 1.0 O3A A:GAV600 3.3 62.4 1.0 C A:ILE328 3.4 41.6 1.0 OD2 A:ASP327 3.4 44.1 1.0 NZ A:LYS442 3.8 45.7 1.0 O2G A:GAV600 4.0 49.0 1.0 O1G A:GAV600 4.1 48.8 1.0 CE A:LYS442 4.1 46.4 1.0 N A:ILE328 4.1 41.4 1.0 CG A:GLU370 4.2 44.3 1.0 MG A:MG602 4.2 52.7 1.0 N A:ASP329 4.3 41.0 1.0 CA A:ASP329 4.3 41.2 1.0 CA A:ILE328 4.3 41.7 1.0 O1B A:GAV600 4.4 52.7 1.0 C A:ASP327 4.4 41.7 1.0 N A:PHE330 4.5 41.1 1.0 CB A:ASP327 4.5 41.1 1.0 C A:ASP329 4.6 41.4 1.0 CB A:PHE331 4.7 41.9 1.0 N A:PHE331 4.7 42.6 1.0 O A:ASP327 4.8 42.7 1.0 PA A:GAV600 4.8 70.4 1.0 CB A:GLU370 4.9 42.8 1.0 CB A:ILE328 5.0 42.1 1.0

Magnesium binding site 3 out of 5 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:52.7 occ:1.00 OE2 A:GLU370 2.2 48.1 1.0 OD2 A:ASP327 2.2 44.1 1.0 CD A:GLU370 3.0 46.5 1.0 OE2 A:GLU371 3.3 53.1 1.0 CG A:GLU370 3.3 44.3 1.0 CG A:ASP327 3.4 42.8 1.0 CD A:GLU371 3.7 46.9 1.0 CG A:GLU371 3.7 44.3 1.0 OD1 A:ASP327 4.0 47.3 1.0 OE1 A:GLU370 4.1 48.2 1.0 MG A:MG601 4.2 45.4 1.0 S1A A:GAV600 4.4 76.2 1.0 CB A:ASP327 4.6 41.1 1.0 OE1 A:GLU371 4.6 50.8 1.0 CB A:GLU370 4.8 42.8 1.0 O3A A:GAV600 4.9 62.4 1.0

Magnesium binding site 4 out of 5 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:36.8 occ:1.00 F2 B:BEF501 2.1 35.0 1.0 OD1 B:ASP10 2.2 46.1 1.0 O B:MET55 2.2 38.5 1.0 O B:HOH2001 2.2 22.7 1.0 OD2 B:ASP53 2.2 31.4 1.0 CG B:ASP10 2.9 43.4 1.0 OD2 B:ASP10 2.9 38.3 1.0 CG B:ASP53 3.4 37.0 1.0 C B:MET55 3.4 40.3 1.0 BE B:BEF501 3.5 39.6 1.0 OD1 B:ASP53 4.0 39.9 1.0 CB B:MET55 4.2 41.2 1.0 CA B:MET55 4.2 41.0 1.0 CB B:ASP10 4.3 41.5 1.0 N B:MET56 4.4 40.7 1.0 F3 B:BEF501 4.4 35.5 1.0 F1 B:BEF501 4.4 39.9 1.0 OD1 B:ASP9 4.5 50.2 1.0 CG B:MET56 4.6 43.3 1.0 N B:MET55 4.6 40.4 1.0 CA B:MET56 4.6 41.6 1.0 CB B:ASP53 4.6 37.0 1.0 N B:ASP10 4.7 40.5 1.0 OD2 B:ASP9 4.8 45.1 1.0 CG B:ASP9 4.8 44.3 1.0 CD1 B:ILE11 4.9 34.8 1.0 CG1 B:ILE11 5.0 36.2 1.0

Magnesium binding site 5 out of 5 in the Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Activated Response Regulator Pled in Complex with C-Digmp and Gtp- Alpha-S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:46.7 occ:1.00 O3G B:GAV600 2.2 42.0 1.0 OD1 B:ASP327 2.2 46.5 1.0 O2B B:GAV600 2.2 53.4 1.0 OE1 B:GLU370 2.2 47.6 1.0 O B:ILE328 2.2 42.8 1.0 OE2 B:GLU370 2.6 48.1 1.0 CD B:GLU370 2.7 46.3 1.0 PB B:GAV600 3.0 56.0 1.0 CG B:ASP327 3.1 42.7 1.0 PG B:GAV600 3.2 38.7 1.0 O3B B:GAV600 3.2 48.3 1.0 O3A B:GAV600 3.3 60.2 1.0 OD2 B:ASP327 3.4 43.8 1.0 C B:ILE328 3.4 41.5 1.0 NZ B:LYS442 3.7 43.8 1.0 O1G B:GAV600 4.1 39.0 1.0 N B:ILE328 4.1 41.7 1.0 CG B:GLU370 4.2 44.2 1.0 O2G B:GAV600 4.2 39.4 1.0 CE B:LYS442 4.3 45.0 1.0 N B:ASP329 4.3 41.0 1.0 CA B:ILE328 4.3 41.8 1.0 CA B:ASP329 4.3 41.4 1.0 O1B B:GAV600 4.4 54.2 1.0 C B:ASP327 4.5 42.0 1.0 CB B:ASP327 4.5 41.1 1.0 N B:PHE330 4.5 41.3 1.0 CB B:PHE331 4.7 42.0 1.0 N B:PHE331 4.7 42.4 1.0 C B:ASP329 4.7 41.4 1.0 O B:ASP327 4.8 42.8 1.0 CB B:GLU370 4.9 42.7 1.0 PA B:GAV600 4.9 65.1 1.0 CB B:ILE328 4.9 42.1 1.0

P.Wassmann, C.Chan, R.Paul, A.Beck, H.Heerklotz, U.Jenal, T.Schirmer. Structure of BEF3--Modified Response Regulator Pled: Implications For Diguanylate Cyclase Activation, Catalysis, and Feedback Inhibition Structure V. 15 915 2007.
ISSN: ISSN 0969-2126
PubMed: 17697997
DOI: 10.1016/J.STR.2007.06.016