Magnesium in PDB 9g86: Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp

All present enzymatic activity of Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp:
2.7.7.65;

The structure of Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp, PDB code: 9g86 was solved by C.Dugelay, C.Jaboulay, M.Guzzo, L.Terradot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.53 / 3.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.571, 132.571, 508.411, 90, 90, 120
R / Rfree (%)	19 / 22.9

The binding sites of Magnesium atom in the Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp (pdb code 9g86). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp, PDB code: 9g86:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:61.1 occ:1.00 OE2 A:GLU370 1.9 61.2 1.0 O A:ILE328 2.2 61.2 1.0 O3G A:0O2502 2.3 79.7 1.0 O3B A:0O2502 2.3 73.0 1.0 OD2 A:ASP327 2.4 71.9 1.0 O3A A:0O2502 2.7 52.7 1.0 CD A:GLU370 2.7 69.7 1.0 PG A:0O2502 2.8 77.3 1.0 PB A:0O2502 2.9 56.6 1.0 OE1 A:GLU370 2.9 93.7 1.0 O1B A:0O2502 3.3 72.5 1.0 C A:ILE328 3.4 64.9 1.0 CG A:ASP327 3.4 66.0 1.0 O1G A:0O2502 3.6 50.1 1.0 PA A:0O2502 3.8 54.3 1.0 OD1 A:ASP327 3.9 65.1 1.0 O2A A:0O2502 4.0 76.4 1.0 O2G A:0O2502 4.1 79.6 1.0 CA A:ASP329 4.1 63.4 1.0 O5' A:0O2502 4.1 67.2 1.0 CG A:GLU370 4.1 54.7 1.0 N A:ASP329 4.2 66.3 1.0 N A:PHE330 4.2 62.3 1.0 O2B A:0O2502 4.3 72.1 1.0 N A:ILE328 4.4 59.6 1.0 CA A:ILE328 4.5 62.1 1.0 CB A:ASP327 4.5 56.5 1.0 C A:ASP329 4.5 64.8 1.0 C A:ASP327 4.6 60.0 1.0 N A:PHE331 4.7 60.2 1.0 O A:ASP327 4.9 64.6 1.0 OD1 A:ASP329 4.9 86.4 1.0 CB A:PHE331 5.0 58.2 1.0

Magnesium binding site 2 out of 4 in the Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:69.7 occ:1.00 OE2 B:GLU370 1.8 72.5 1.0 O2B B:0O2504 2.3 82.8 1.0 O3B B:0O2504 2.5 81.9 1.0 O3G B:0O2504 2.6 67.9 1.0 O B:ILE328 2.6 64.8 1.0 NZ B:LYS442 2.7 85.4 1.0 CD B:GLU370 2.7 75.9 1.0 PG B:0O2504 2.7 74.5 1.0 O1A B:0O2504 2.7 65.3 1.0 PB B:0O2504 2.7 60.5 1.0 O2G B:0O2504 2.9 81.7 1.0 OE1 B:GLU370 3.0 84.7 1.0 O3A B:0O2504 3.3 66.4 1.0 OD2 B:ASP327 3.3 96.7 1.0 PA B:0O2504 3.5 61.6 1.0 C B:ILE328 3.8 65.5 1.0 CG B:ASP327 3.9 90.3 1.0 CG B:GLU370 4.1 60.6 1.0 CE B:LYS442 4.1 81.1 1.0 O1B B:0O2504 4.2 77.6 1.0 O1G B:0O2504 4.2 92.7 1.0 OD1 B:ASP327 4.2 94.2 1.0 CA B:ASP329 4.4 71.6 1.0 N B:PHE330 4.4 65.3 1.0 O5' B:0O2504 4.5 69.2 1.0 N B:ASP329 4.6 64.4 1.0 O2A B:0O2504 4.7 99.8 1.0 CB B:ASP327 4.8 69.9 1.0 N B:ILE328 4.8 51.9 1.0 C B:ASP329 4.8 67.4 1.0 CD B:LYS442 4.8 69.3 1.0 CA B:ILE328 4.9 57.8 1.0 N B:PHE331 4.9 63.8 1.0 C B:ASP327 4.9 54.6 1.0

Magnesium binding site 3 out of 4 in the Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:57.5 occ:1.00 OE1 C:GLU370 2.1 61.8 1.0 O3B C:0O2502 2.4 76.7 1.0 OD2 C:ASP327 2.4 72.8 1.0 O C:ILE328 2.6 64.2 1.0 OE2 C:GLU370 2.6 82.7 1.0 O2B C:0O2502 2.7 83.0 1.0 PB C:0O2502 2.7 66.4 1.0 CD C:GLU370 2.7 72.9 1.0 O3G C:0O2502 2.8 66.7 1.0 O3A C:0O2502 2.8 63.6 1.0 PG C:0O2502 2.9 69.7 1.0 O2A C:0O2502 3.0 73.9 1.0 O2G C:0O2502 3.2 75.2 1.0 PA C:0O2502 3.3 60.8 1.0 NZ C:LYS442 3.3 67.6 1.0 CG C:ASP327 3.5 71.2 1.0 O1A C:0O2502 3.7 66.6 1.0 C C:ILE328 3.8 65.2 1.0 OD1 C:ASP327 4.0 75.4 1.0 CG C:GLU370 4.2 74.6 1.0 O1B C:0O2502 4.2 66.7 1.0 O1G C:0O2502 4.3 81.1 1.0 CE C:LYS442 4.4 75.2 1.0 CA C:ASP329 4.6 59.8 1.0 N C:PHE330 4.6 68.8 1.0 N C:ASP329 4.6 63.0 1.0 N C:ILE328 4.6 54.9 1.0 CB C:ASP327 4.7 51.8 1.0 CA C:ILE328 4.7 54.2 1.0 CB C:GLU370 4.7 54.4 1.0 C C:ASP327 4.8 56.8 1.0 N C:PHE331 4.9 62.1 1.0 O5' C:0O2502 4.9 85.2 1.0 C C:ASP329 4.9 66.5 1.0

Magnesium binding site 4 out of 4 in the Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg505 b:75.2 occ:1.00 O2G D:0O2502 2.1 80.4 1.0 OE1 D:GLU370 2.2 76.8 1.0 O D:ILE328 2.2 74.0 1.0 O3A D:0O2502 2.2 69.3 1.0 OD2 D:ASP327 2.2 79.0 1.0 OE2 D:GLU370 2.3 94.1 1.0 CD D:GLU370 2.5 92.3 1.0 O3B D:0O2502 2.9 81.2 1.0 PG D:0O2502 3.0 80.4 1.0 NZ D:LYS442 3.0 89.3 1.0 PB D:0O2502 3.1 73.7 1.0 CG D:ASP327 3.3 74.5 1.0 C D:ILE328 3.4 76.1 1.0 PA D:0O2502 3.5 70.6 1.0 O1A D:0O2502 3.7 84.9 1.0 O1G D:0O2502 3.7 82.5 1.0 O1B D:0O2502 3.9 71.6 1.0 OD1 D:ASP327 4.0 89.0 1.0 CG D:GLU370 4.0 79.8 1.0 O3G D:0O2502 4.2 70.5 1.0 N D:ILE328 4.2 56.9 1.0 CE D:LYS442 4.2 88.0 1.0 N D:ASP329 4.3 76.4 1.0 CA D:ASP329 4.3 75.1 1.0 O2B D:0O2502 4.3 83.4 1.0 CB D:ASP327 4.4 63.4 1.0 CA D:ILE328 4.4 60.3 1.0 O2A D:0O2502 4.4 67.6 1.0 C D:ASP327 4.5 65.7 1.0 N D:PHE330 4.5 72.8 1.0 O5' D:0O2502 4.7 71.8 1.0 CB D:GLU370 4.7 60.7 1.0 C D:ASP329 4.8 79.3 1.0 O D:ASP327 4.8 67.3 1.0 CA D:ASP327 4.9 64.6 1.0 CB D:ILE328 4.9 52.6 1.0 N D:PHE331 5.0 68.8 1.0

C.Dugelay, C.Jaboulay, M.Guzzo, L.Terradot. Structure of Response Regulator Pled in Complex with C-Digmp and Pppgpp To Be Published.