Magnesium in PDB 8c05: Lov-Activated Diguanylate Cyclase, Dark-State Structure

The structure of Lov-Activated Diguanylate Cyclase, Dark-State Structure, PDB code: 8c05 was solved by U.Vide, A.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.80 / 2.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.35, 56.35, 318.04, 90, 90, 120
R / Rfree (%)	25.5 / 29.8

The binding sites of Magnesium atom in the Lov-Activated Diguanylate Cyclase, Dark-State Structure (pdb code 8c05). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Lov-Activated Diguanylate Cyclase, Dark-State Structure, PDB code: 8c05:

Magnesium binding site 1 out of 1 in the Lov-Activated Diguanylate Cyclase, Dark-State Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lov-Activated Diguanylate Cyclase, Dark-State Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:148.7 occ:1.00 OD2 A:ASP185 2.1 139.1 1.0 OE1 A:GLU229 2.1 131.2 1.0 O A:ILE186 2.4 122.6 1.0 OE2 A:GLU229 2.5 149.6 1.0 CD A:GLU229 2.5 133.4 1.0 O3 A:DPO402 2.6 159.3 1.0 P1 A:DPO402 3.1 174.4 1.0 O4 A:DPO402 3.1 187.2 1.0 O7 A:DPO402 3.1 169.3 1.0 CG A:ASP185 3.1 130.1 1.0 O2 A:DPO402 3.2 162.3 1.0 C A:ILE186 3.6 120.7 1.0 OD1 A:ASP185 3.6 131.6 1.0 NZ A:LYS301 3.7 120.7 1.0 P2 A:DPO402 3.7 195.6 1.0 CG A:GLU229 3.9 123.2 1.0 N A:ILE186 4.1 106.4 1.0 CB A:ASP185 4.4 119.7 1.0 CA A:ILE186 4.4 105.1 1.0 O1 A:DPO402 4.5 166.3 1.0 N A:ASP187 4.6 113.8 1.0 CB A:PHE189 4.6 124.6 1.0 CE A:LYS301 4.6 121.9 1.0 C A:ASP185 4.7 108.7 1.0 CB A:GLU229 4.7 117.0 1.0 CA A:ASP187 4.7 118.5 1.0 O6 A:DPO402 4.7 181.3 1.0 O5 A:DPO402 4.8 180.2 1.0 N A:PHE189 4.8 121.0 1.0 N A:TYR188 4.9 119.5 1.0 CB A:ILE186 4.9 103.3 1.0 CA A:ASP185 5.0 112.3 1.0

U.Vide, D.Kasapovic, M.Fuchs, M.P.Heimboeck, M.G.Totaro, E.Zenzmaier, A.Winkler. Illuminating the Inner Workings of A Natural Protein Switch: Blue-Light Sensing in Lov-Activated Diguanylate Cyclases Sci Adv 2023.
ISSN: ESSN 2375-2548