Magnesium in PDB 1w25: Response Regulator Pled in Complex with C-Digmp

The structure of Response Regulator Pled in Complex with C-Digmp, PDB code: 1w25 was solved by C.Chan, T.Schirmer, U.Jenal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	135.870, 135.870, 169.247, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 23.9

The structure of Response Regulator Pled in Complex with C-Digmp also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Response Regulator Pled in Complex with C-Digmp (pdb code 1w25). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Response Regulator Pled in Complex with C-Digmp, PDB code: 1w25:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Response Regulator Pled in Complex with C-Digmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Response Regulator Pled in Complex with C-Digmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:43.4 occ:1.00 OD1 A:ASP10 2.3 33.0 1.0 O A:MET55 2.3 29.3 1.0 OD2 A:ASP53 2.5 34.9 1.0 OD1 A:ASP9 2.6 37.1 1.0 CG A:ASP53 3.4 29.4 1.0 C A:MET55 3.5 28.5 1.0 CG A:ASP10 3.6 29.3 1.0 CG A:ASP9 3.7 28.9 1.0 CB A:MET55 3.7 30.2 1.0 OD2 A:ASP9 4.1 35.2 1.0 CA A:MET55 4.1 29.9 1.0 CD1 A:ILE11 4.1 30.0 1.0 OD2 A:ASP10 4.2 32.0 1.0 CB A:ASP53 4.2 26.8 1.0 OD1 A:ASP53 4.2 35.2 1.0 N A:ASP10 4.2 25.9 1.0 N A:MET55 4.5 28.8 1.0 CE A:MET55 4.5 37.3 1.0 CG A:MET56 4.5 28.1 1.0 N A:MET56 4.6 27.1 1.0 CG1 A:ILE11 4.6 29.7 1.0 CB A:ASP10 4.7 26.7 1.0 CA A:MET56 4.9 26.7 1.0 NZ A:LYS105 4.9 40.0 1.0 CA A:ASP10 4.9 27.0 1.0 CB A:ASP9 5.0 26.1 1.0 N A:ILE11 5.0 28.4 1.0

Magnesium binding site 2 out of 2 in the Response Regulator Pled in Complex with C-Digmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Response Regulator Pled in Complex with C-Digmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:39.9 occ:1.00 OD1 B:ASP10 2.2 32.7 1.0 OD1 B:ASP9 2.4 37.4 1.0 O B:MET55 2.4 29.2 1.0 OD2 B:ASP53 2.4 34.9 1.0 CG B:ASP53 3.4 29.4 1.0 CG B:ASP10 3.4 29.2 1.0 C B:MET55 3.6 28.4 1.0 CG B:ASP9 3.6 28.9 1.0 CB B:MET55 3.9 30.4 1.0 OD2 B:ASP9 4.0 35.0 1.0 N B:ASP10 4.0 25.9 1.0 CB B:ASP53 4.1 27.0 1.0 OD2 B:ASP10 4.1 32.0 1.0 CD1 B:ILE11 4.2 30.0 1.0 OD1 B:ASP53 4.2 35.1 1.0 CA B:MET55 4.2 29.9 1.0 CG B:MET56 4.4 28.0 1.0 CB B:ASP10 4.5 26.8 1.0 N B:MET55 4.6 28.7 1.0 CG1 B:ILE11 4.6 29.7 1.0 N B:MET56 4.6 27.0 1.0 CE B:MET55 4.7 37.4 1.0 CA B:ASP10 4.7 27.1 1.0 CB B:ASP9 4.8 26.0 1.0 N B:ILE11 4.8 28.3 1.0 CA B:ASP9 4.8 25.4 1.0 CA B:MET56 4.9 26.7 1.0 C B:ASP9 4.9 25.0 1.0 NZ B:LYS105 4.9 40.0 1.0

C.Chan, R.Paul, D.Samoray, N.Amiot, B.Giese, U.Jenal, T.Schirmer. Structural Basis of Activity and Allosteric Control of Diguanylate Cyclase Proc.Natl.Acad.Sci.Usa V. 101 17084 2004.
ISSN: ISSN 0027-8424
PubMed: 15569936
DOI: 10.1073/PNAS.0406134101