Magnesium in PDB 3n3t: Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp

The structure of Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp, PDB code: 3n3t was solved by C.Chang, X.Xu, H.Cui, A.Savchenko, A.Edwards, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.96 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.560, 63.201, 173.987, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 25.4

The structure of Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp (pdb code 3n3t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp, PDB code: 3n3t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with 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 Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:36.0 occ:1.00 O11 A:C2E801 1.8 62.1 1.0 OD1 A:ASN584 1.9 26.7 1.0 OE2 A:GLU523 2.0 24.5 1.0 OD2 A:ASP646 2.2 28.5 1.0 OE1 A:GLU616 2.2 30.8 1.0 O A:HOH1 2.3 20.7 1.0 CG A:ASN584 2.9 27.1 1.0 CD A:GLU523 3.1 24.2 1.0 P11 A:C2E801 3.1 62.8 1.0 CG A:ASP646 3.2 27.2 1.0 ND2 A:ASN584 3.3 26.1 1.0 CD A:GLU616 3.4 31.3 1.0 OD1 A:ASP646 3.5 30.7 1.0 OE1 A:GLU523 3.7 26.2 1.0 O21 A:C2E801 3.8 63.0 1.0 O5A A:C2E801 3.8 64.5 1.0 CB A:GLU616 4.2 28.7 1.0 NZ A:LYS667 4.2 25.1 1.0 OE2 A:GLU616 4.3 33.2 1.0 CG A:GLU523 4.3 23.6 1.0 CB A:ASN584 4.3 26.6 1.0 O A:HOH84 4.3 63.0 1.0 O3' A:C2E801 4.3 62.6 1.0 O A:HOH20 4.4 37.0 1.0 CG A:GLU616 4.4 30.3 1.0 CB A:ASP646 4.5 25.9 1.0 C2' A:C2E801 4.5 60.6 1.0 C5A A:C2E801 4.6 66.1 1.0 MG A:MG803 4.7 62.3 1.0 C3' A:C2E801 4.7 62.3 1.0 O2' A:C2E801 4.8 56.5 1.0 CA A:ASN584 4.9 26.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with 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 Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:62.3 occ:1.00 OE1 A:GLU703 2.1 39.5 1.0 O21 A:C2E801 2.2 63.0 1.0 O A:HOH24 2.5 52.0 1.0 OD1 A:ASP647 2.5 35.9 1.0 OD1 A:ASP646 2.6 30.7 1.0 CD A:GLU703 3.1 37.8 1.0 N A:ASP647 3.3 26.2 1.0 OE2 A:GLU703 3.4 39.7 1.0 CG A:ASP647 3.4 32.2 1.0 O A:HOH84 3.4 63.0 1.0 CG A:ASP646 3.5 27.2 1.0 P11 A:C2E801 3.6 62.8 1.0 CA A:ASP647 3.6 27.3 1.0 O A:HOH1 3.7 20.7 1.0 OD1 A:ASP669 3.7 29.2 1.0 OD2 A:ASP646 4.0 28.5 1.0 CB A:ASP647 4.1 28.3 1.0 O5A A:C2E801 4.1 64.5 1.0 O11 A:C2E801 4.2 62.1 1.0 OD2 A:ASP647 4.2 37.3 1.0 C A:ASP646 4.3 25.5 1.0 CG A:GLU703 4.4 31.9 1.0 CB A:ASP646 4.5 25.9 1.0 NE2 A:GLN670 4.6 42.6 1.0 O3' A:C2E801 4.7 62.6 1.0 CA A:ASP646 4.7 25.4 1.0 MG A:MG802 4.7 36.0 1.0 CG A:ASP669 4.8 26.6 1.0 CA A:ASP669 4.9 26.2 1.0 C A:ASP647 5.0 27.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp


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 Complex with Cyclic Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:30.4 occ:1.00 O11 B:C2E801 2.0 41.2 1.0 O B:HOH209 2.1 21.4 1.0 OE1 B:GLU616 2.2 30.6 1.0 OD2 B:ASP646 2.2 27.5 1.0 OD1 B:ASN584 2.2 26.2 1.0 OE2 B:GLU523 2.2 28.7 1.0 CD B:GLU523 3.0 26.7 1.0 CG B:ASN584 3.1 25.7 1.0 CG B:ASP646 3.1 25.7 1.0 P11 B:C2E801 3.2 42.5 1.0 ND2 B:ASN584 3.3 27.1 1.0 CD B:GLU616 3.4 29.8 1.0 OE1 B:GLU523 3.4 29.8 1.0 OD1 B:ASP646 3.4 26.3 1.0 O21 B:C2E801 3.7 43.4 1.0 O5A B:C2E801 3.8 42.1 1.0 NZ B:LYS667 4.0 23.6 1.0 MG B:MG803 4.1 42.5 1.0 OE2 B:GLU616 4.2 32.2 1.0 CG B:GLU523 4.2 23.4 1.0 O B:HOH152 4.2 31.9 1.0 CB B:GLU616 4.3 25.8 1.0 O B:HOH142 4.3 34.0 1.0 CB B:ASP646 4.4 24.6 1.0 CG B:GLU616 4.4 28.0 1.0 O3' B:C2E801 4.5 42.2 1.0 CB B:ASN584 4.5 25.9 1.0 OE1 B:GLU703 4.6 30.6 1.0 C5A B:C2E801 4.7 42.9 1.0 CD B:LYS667 4.8 24.2 1.0 C2' B:C2E801 4.9 40.4 1.0 C3' B:C2E801 4.9 42.3 1.0 CE B:LYS667 5.0 23.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Putative Diguanylate Cyclase/Phosphodiesterase Complex with Cyclic Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:42.5 occ:1.00 O21 B:C2E801 1.8 43.4 1.0 OE2 B:GLU703 2.1 34.5 1.0 OD1 B:ASP646 2.2 26.3 1.0 OE1 B:GLU703 2.3 30.6 1.0 OD1 B:ASP647 2.3 32.6 1.0 CD B:GLU703 2.5 31.5 1.0 O B:HOH206 2.7 38.6 1.0 O B:HOH209 3.1 21.4 1.0 P11 B:C2E801 3.1 42.5 1.0 CG B:ASP646 3.3 25.7 1.0 O5A B:C2E801 3.3 42.1 1.0 CG B:ASP647 3.5 30.3 1.0 OD2 B:ASP646 3.7 27.5 1.0 O11 B:C2E801 3.8 41.2 1.0 N B:ASP647 3.8 25.4 1.0 O B:HOH172 3.9 52.6 1.0 CG B:GLU703 4.0 28.1 1.0 O B:HOH152 4.1 31.9 1.0 MG B:MG802 4.1 30.4 1.0 OD2 B:ASP647 4.1 35.2 1.0 O3' B:C2E801 4.3 42.2 1.0 CA B:ASP647 4.3 26.3 1.0 CB B:ASP647 4.5 26.3 1.0 CB B:ASP646 4.6 24.6 1.0 C5A B:C2E801 4.6 42.9 1.0 OE1 B:GLN670 4.7 36.3 1.0 OD1 B:ASP669 4.7 32.7 1.0 C B:ASP646 4.7 25.1 1.0 CB B:GLU703 4.8 25.9 1.0 CA B:ASP646 4.9 24.8 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