Magnesium in PDB 2r6o: Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans

The structure of Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans, PDB code: 2r6o was solved by C.Chang, X.Xu, H.Zheng, A.Savchenko, A.M.Edwards, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.70 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.051, 63.141, 173.282, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.8

The structure of Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans (pdb code 2r6o). 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 Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans, PDB code: 2r6o:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans


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 Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:20.8 occ:1.00 OD1 A:ASN584 2.0 26.2 1.0 OE2 A:GLU523 2.1 23.8 1.0 OE1 A:GLU616 2.1 26.5 1.0 OD2 A:ASP646 2.1 25.6 1.0 O A:HOH12 2.1 23.5 1.0 O A:HOH1 2.2 21.1 1.0 CG A:ASN584 3.0 26.3 1.0 CD A:GLU523 3.0 28.1 1.0 CG A:ASP646 3.1 26.8 1.0 CD A:GLU616 3.3 25.4 1.0 OD1 A:ASP646 3.4 27.6 1.0 ND2 A:ASN584 3.4 26.6 1.0 OE1 A:GLU523 3.6 27.6 1.0 CB A:GLU616 3.9 26.0 1.0 O A:HOH135 4.0 35.1 1.0 CG A:GLU523 4.1 24.6 1.0 O A:HOH45 4.2 29.1 1.0 NZ A:LYS667 4.2 24.2 1.0 CG A:GLU616 4.2 27.1 1.0 OE2 A:GLU616 4.2 29.6 1.0 O A:HOH62 4.2 30.1 1.0 OE2 A:GLU703 4.4 42.4 1.0 CB A:ASN584 4.4 25.6 1.0 O A:HOH32 4.4 27.9 1.0 CB A:ASP646 4.4 25.5 1.0 O A:HOH254 4.6 47.2 1.0 O A:HOH41 4.6 30.4 1.0 CD A:LYS667 4.8 23.1 1.0 CA A:ASN584 5.0 26.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans


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 Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:23.4 occ:1.00 OE1 B:GLU616 2.1 24.3 1.0 OD1 B:ASN584 2.1 25.4 1.0 O B:HOH11 2.1 23.4 1.0 OE2 B:GLU523 2.1 30.9 1.0 OD2 B:ASP646 2.1 23.0 1.0 O B:HOH9 2.2 23.3 1.0 CG B:ASN584 3.1 26.9 1.0 CD B:GLU523 3.1 29.6 1.0 CG B:ASP646 3.1 26.1 1.0 O B:HOH30 3.2 28.1 1.0 CD B:GLU616 3.3 27.2 1.0 ND2 B:ASN584 3.4 28.6 1.0 OD1 B:ASP646 3.4 25.6 1.0 OE1 B:GLU523 3.6 31.2 1.0 CB B:GLU616 3.9 25.1 1.0 O B:HOH119 4.0 35.1 1.0 NZ B:LYS667 4.1 26.1 1.0 CG B:GLU523 4.1 29.6 1.0 OE2 B:GLU616 4.2 30.0 1.0 CG B:GLU616 4.2 26.5 1.0 OE2 B:GLU703 4.3 38.1 0.5 O B:HOH118 4.4 35.7 1.0 CB B:ASP646 4.4 24.6 1.0 CB B:ASN584 4.4 26.9 1.0 CD B:LYS667 4.6 25.1 1.0 O B:HOH106 4.6 34.0 1.0 O B:HOH143 4.7 37.2 1.0 OE2 B:GLU703 4.9 27.6 0.5 OE1 B:GLU703 4.9 36.1 0.5 CE B:LYS667 4.9 25.3 1.0 CD B:GLU703 5.0 35.3 0.5 O B:HOH154 5.0 37.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans


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 Putative Diguanylate Cyclase/Phosphodiesterase From Thiobacillus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:38.0 occ:1.00 O B:HOH139 1.9 37.9 1.0 OD1 B:ASP669 2.1 27.5 1.0 O B:HOH34 2.2 43.9 1.0 O B:HOH229 2.2 41.0 1.0 O B:HOH378 2.3 48.4 1.0 OD1 B:ASP647 2.4 30.6 1.0 CG B:ASP669 3.1 27.8 1.0 CG B:ASP647 3.3 28.9 1.0 OD2 B:ASP669 3.5 27.5 1.0 CB B:ASP647 3.5 24.8 1.0 O B:HOH323 4.0 51.4 1.0 CA B:ASP647 4.1 24.7 1.0 O B:HOH119 4.1 35.1 1.0 OD2 B:ASP647 4.3 29.6 1.0 OG1 B:THR650 4.4 25.2 1.0 CB B:ASP669 4.4 26.7 1.0 OE1 B:GLU703 4.4 26.9 0.5 NE2 B:GLN670 4.5 33.2 0.5 NE2 B:GLN670 4.6 35.8 0.5 CG2 B:THR650 4.8 27.4 1.0 CG B:GLN670 4.9 31.2 0.5 O B:HOH111 5.0 35.5 1.0

A.Tchigvintsev, X.Xu, A.Singer, C.Chang, G.Brown, M.Proudfoot, H.Cui, R.Flick, W.F.Anderson, A.Joachimiak, M.Y.Galperin, A.Savchenko, A.F.Yakunin. Structural Insight Into the Mechanism of C-Di-Gmp Hydrolysis By Eal Domain Phosphodiesterases. J.Mol.Biol. V. 402 524 2010.
ISSN: ISSN 0022-2836
PubMed: 20691189
DOI: 10.1016/J.JMB.2010.07.050