Magnesium in PDB 5llx: Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound

All present enzymatic activity of Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound:
2.7.7.65;

The structure of Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound, PDB code: 5llx was solved by G.Gourinchas, A.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.08 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.730, 78.640, 452.040, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 27

The structure of Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound (pdb code 5llx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound, PDB code: 5llx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:89.4 occ:1.00 OE2 A:GLU607 1.8 0.8 1.0 OD1 A:ASP564 2.0 0.2 1.0 O1B A:GTP703 2.0 82.7 1.0 O A:LEU565 2.0 0.1 1.0 O1G A:GTP703 2.2 0.7 1.0 O1A A:GTP703 2.2 75.0 1.0 CD A:GLU607 2.7 0.9 1.0 CG A:ASP564 3.0 0.8 1.0 PB A:GTP703 3.1 71.3 1.0 C A:LEU565 3.2 93.6 1.0 OE1 A:GLU607 3.3 0.7 1.0 PG A:GTP703 3.4 0.1 1.0 PA A:GTP703 3.4 77.0 1.0 OD2 A:ASP564 3.4 92.1 1.0 O3B A:GTP703 3.5 93.6 1.0 O3A A:GTP703 3.6 91.3 1.0 N A:LEU565 3.7 76.3 1.0 CG A:GLU607 3.8 88.8 1.0 CA A:LEU565 3.9 77.8 1.0 O5' A:GTP703 4.0 83.1 1.0 O2G A:GTP703 4.1 95.0 1.0 NZ A:LYS673 4.1 0.5 1.0 N A:ASP566 4.3 0.6 1.0 CB A:ASP564 4.3 80.0 1.0 O2B A:GTP703 4.3 78.8 1.0 CB A:LEU565 4.4 75.7 1.0 C A:ASP564 4.4 81.8 1.0 O2A A:GTP703 4.6 94.9 1.0 CA A:ASP566 4.6 0.8 1.0 O3G A:GTP703 4.6 70.9 1.0 N A:LYS567 4.8 0.7 1.0 CB A:PHE568 4.8 70.9 1.0 CA A:ASP564 4.9 75.7 1.0 N A:PHE568 5.0 88.4 1.0 C A:ASP566 5.0 0.7 1.0

Magnesium binding site 2 out of 2 in the Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacteriophytochrome Activated Diguanylyl Cyclase From Idiomarina Species A28L with Gtp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:0.6 occ:1.00 OE2 B:GLU607 1.8 0.1 1.0 O1B B:GTP703 1.9 0.3 1.0 OD1 B:ASP564 1.9 0.2 1.0 O1G B:GTP703 2.2 0.4 1.0 O B:LEU565 2.2 0.1 1.0 O1A B:GTP703 2.5 0.3 1.0 CD B:GLU607 2.9 0.9 1.0 CG B:ASP564 2.9 0.7 1.0 PB B:GTP703 3.0 0.7 1.0 PG B:GTP703 3.2 0.6 1.0 O3B B:GTP703 3.2 95.1 1.0 OD2 B:ASP564 3.3 0.9 1.0 C B:LEU565 3.4 0.7 1.0 CG B:GLU607 3.6 0.4 1.0 PA B:GTP703 3.6 0.9 1.0 O3A B:GTP703 3.7 0.9 1.0 OE1 B:GLU607 3.9 0.6 1.0 N B:LEU565 3.9 90.8 1.0 O3G B:GTP703 4.0 0.8 1.0 CA B:LEU565 4.1 90.2 1.0 O2B B:GTP703 4.2 0.8 1.0 CB B:ASP564 4.3 0.7 1.0 NZ B:LYS673 4.3 0.6 1.0 O5' B:GTP703 4.3 99.5 1.0 O2G B:GTP703 4.4 0.0 1.0 N B:ASP566 4.4 0.4 1.0 C B:ASP564 4.5 95.3 1.0 CA B:ASP566 4.6 0.4 1.0 CE B:LYS673 4.7 0.2 1.0 CB B:LEU565 4.7 86.3 1.0 O2A B:GTP703 4.8 0.4 1.0 N B:LYS567 4.8 0.6 1.0 CB B:GLU607 4.8 98.4 1.0 CB B:PHE568 4.9 0.1 1.0 CA B:ASP564 4.9 90.5 1.0 N B:PHE568 5.0 0.2 1.0

G.Gourinchas, S.Etzl, C.Gobl, U.Vide, T.Madl, A.Winkler. Long-Range Allosteric Signaling in Red Light-Regulated Diguanylyl Cyclases. Sci Adv V. 3 02498 2017.
ISSN: ESSN 2375-2548
PubMed: 28275738
DOI: 10.1126/SCIADV.1602498