Magnesium in PDB 6rgy: Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5

The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5, PDB code: 6rgy was solved by C.Mideros-Mora, P.Casino, A.Marina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.11 / 2.20
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.470, 92.710, 174.522, 90.00, 93.39, 90.00
R / Rfree (%)	18.6 / 22.7

The structure of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5 (pdb code 6rgy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5, PDB code: 6rgy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:42.9 occ:1.00 F1 C:BFD53 1.8 43.8 1.0 O C:HOH327 1.9 38.1 1.0 OD1 C:ASP10 2.0 45.1 1.0 O C:MET55 2.1 39.2 1.0 OD2 C:BFD53 2.2 40.2 1.0 O C:HOH311 2.3 48.5 1.0 CG C:ASP10 3.0 46.8 1.0 CG C:BFD53 3.2 37.8 1.0 C C:MET55 3.3 40.2 1.0 BE C:BFD53 3.4 39.9 1.0 OD2 C:ASP10 3.4 50.2 1.0 OD1 C:BFD53 3.5 33.9 1.0 O A:HOH684 3.9 43.8 1.0 O A:HOH680 4.0 47.0 1.0 OD1 C:ASP9 4.0 41.1 1.0 CA C:MET55 4.1 39.9 1.0 CB C:MET55 4.2 44.1 1.0 N C:MET56 4.3 42.6 1.0 CG C:MET56 4.3 42.8 1.0 N C:ASP10 4.3 39.2 1.0 CB C:ASP10 4.4 47.8 1.0 N C:MET55 4.4 38.7 1.0 F2 C:BFD53 4.4 42.5 1.0 CB C:BFD53 4.5 34.4 1.0 F3 C:BFD53 4.5 46.4 1.0 CA C:MET56 4.6 44.7 1.0 CG C:ASP9 4.7 41.0 1.0 CA C:ASP10 4.8 46.2 1.0 OD2 C:ASP9 4.9 44.0 1.0

Magnesium binding site 2 out of 2 in the Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Revisiting pH-Gated Conformational Switch. Complex HK853-RR468 pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:41.3 occ:1.00 F1 D:BFD53 1.9 38.9 1.0 OD2 D:BFD53 1.9 41.1 1.0 OD1 D:ASP10 2.0 46.2 1.0 O D:HOH327 2.0 39.8 1.0 O D:MET55 2.1 36.5 1.0 O D:HOH319 2.1 38.0 1.0 CG D:BFD53 3.0 39.6 1.0 CG D:ASP10 3.0 46.3 1.0 OD1 D:BFD53 3.3 38.2 1.0 BE D:BFD53 3.3 38.0 1.0 C D:MET55 3.3 41.5 1.0 OD2 D:ASP10 3.4 47.0 1.0 OD1 D:ASP9 3.7 42.6 1.0 O B:HOH678 4.0 46.9 1.0 O B:HOH671 4.1 48.5 1.0 CG D:MET56 4.2 42.9 1.0 CA D:MET55 4.2 42.1 1.0 N D:ASP10 4.2 40.9 1.0 O B:HOH657 4.3 58.2 1.0 CB D:ASP10 4.3 46.7 1.0 CB D:BFD53 4.3 36.8 1.0 N D:MET55 4.3 39.3 1.0 CB D:MET55 4.3 47.3 1.0 N D:MET56 4.3 43.1 1.0 F2 D:BFD53 4.3 41.1 1.0 CG D:ASP9 4.4 42.0 1.0 F3 D:BFD53 4.5 46.4 1.0 CA D:MET56 4.5 45.0 1.0 CA D:ASP10 4.7 45.2 1.0 OD2 D:ASP9 4.8 44.1 1.0 CB D:MET56 4.9 44.0 1.0 NZ D:LYS105 4.9 40.8 1.0 N D:SER11 5.0 40.9 1.0

C.Mideros-Mora, L.Miguel-Romero, A.Felipe-Ruiz, P.Casino, A.Marina. Revisiting the pH-Gated Conformational Switch on the Activities of Hiska-Family Histidine Kinases. Nat Commun V. 11 769 2020.
ISSN: ESSN 2041-1723
PubMed: 32034139
DOI: 10.1038/S41467-020-14540-5