Magnesium in PDB 9by5: Crystal Structure of Rt-Phyr (RUTHE_01174)

The structure of Crystal Structure of Rt-Phyr (RUTHE_01174), PDB code: 9by5 was solved by D.Swingle, E.A.Isiorho, K.H.Gardner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.00 / 1.99
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.91, 118.642, 121.088, 90, 90, 90
R / Rfree (%)	20.9 / 23.7

The structure of Crystal Structure of Rt-Phyr (RUTHE_01174) also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Rt-Phyr (RUTHE_01174) (pdb code 9by5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Rt-Phyr (RUTHE_01174), PDB code: 9by5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Rt-Phyr (RUTHE_01174)


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 Rt-Phyr (RUTHE_01174) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:43.7 occ:1.00 O A:HOH416 2.0 51.3 1.0 O A:GLN199 2.0 51.0 1.0 OD1 A:ASP153 2.0 41.9 1.0 O A:HOH407 2.0 44.4 1.0 OD2 A:ASP197 2.1 43.8 1.0 O A:HOH434 2.2 41.4 1.0 CG A:ASP153 3.0 50.6 1.0 CG A:ASP197 3.1 40.6 1.0 C A:GLN199 3.2 51.9 1.0 OD2 A:ASP153 3.3 50.1 1.0 HB3 A:GLN199 3.5 74.0 1.0 H A:ASP153 3.6 43.8 1.0 OD1 A:ASP197 3.6 46.2 1.0 HA A:LEU200 3.7 59.0 1.0 HD23 A:LEU200 3.8 48.3 1.0 OE2 A:GLU152 3.8 43.5 1.0 HG3 A:GLU154 3.9 71.8 1.0 H A:GLN199 4.0 58.7 1.0 CA A:GLN199 4.1 54.9 1.0 N A:LEU200 4.2 44.4 1.0 H A:GLU154 4.2 46.4 1.0 CB A:GLN199 4.3 61.6 1.0 N A:GLN199 4.3 48.8 1.0 CA A:LEU200 4.4 49.0 1.0 CB A:ASP153 4.4 41.3 1.0 N A:ASP153 4.4 36.4 1.0 CB A:ASP197 4.4 38.9 1.0 HB3 A:ASP197 4.4 46.8 1.0 HZ2 A:LYS246 4.4 61.9 1.0 HZ1 A:LYS246 4.6 61.9 1.0 OE2 A:GLU154 4.6 67.5 1.0 HB3 A:ASP153 4.6 49.7 1.0 CD A:GLU152 4.7 39.8 1.0 OE1 A:GLN199 4.8 103.5 1.0 CD2 A:LEU200 4.8 40.2 1.0 HB2 A:ASP197 4.8 46.8 1.0 N A:GLU154 4.8 38.5 1.0 CG A:GLU154 4.8 59.8 1.0 HA A:GLU152 4.8 44.8 1.0 CD A:GLN199 4.9 92.4 1.0 NZ A:LYS246 4.9 51.5 1.0 CA A:ASP153 4.9 41.5 1.0 HB2 A:GLN199 4.9 74.0 1.0 HZ3 A:LYS246 4.9 61.9 1.0 C A:LEU200 4.9 49.6 1.0 H A:ILE198 5.0 52.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Rt-Phyr (RUTHE_01174)


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 Rt-Phyr (RUTHE_01174) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:47.3 occ:1.00 OD1 B:ASP153 1.9 47.2 1.0 OD2 B:ASP197 1.9 48.9 1.0 O B:HOH416 2.0 46.4 1.0 O B:GLN199 2.0 44.7 1.0 O B:HOH417 2.1 46.8 1.0 CG B:ASP153 2.9 45.0 1.0 CG B:ASP197 3.1 49.2 1.0 C B:GLN199 3.2 47.5 1.0 OD2 B:ASP153 3.3 49.5 1.0 OD1 B:ASP197 3.6 49.6 1.0 H B:ASP153 3.6 45.5 1.0 HA B:LEU200 3.7 58.2 1.0 HB3 B:GLN199 3.7 70.4 1.0 H B:GLN199 3.8 56.4 1.0 HG3 B:GLU154 3.9 67.3 1.0 HD23 B:LEU200 4.0 53.7 1.0 CA B:GLN199 4.1 55.9 1.0 HG2 B:GLN199 4.1 75.7 1.0 N B:GLN199 4.2 46.9 1.0 N B:LEU200 4.2 43.0 1.0 CB B:ASP153 4.2 45.4 1.0 CB B:GLN199 4.3 58.6 1.0 OE2 B:GLU152 4.3 40.6 1.0 HB3 B:ASP197 4.3 50.1 1.0 H B:GLU154 4.3 46.6 1.0 CB B:ASP197 4.3 41.7 1.0 CA B:LEU200 4.3 48.4 1.0 HZ1 B:LYS246 4.4 60.4 1.0 N B:ASP153 4.4 37.8 1.0 HB3 B:ASP153 4.4 54.6 1.0 HZ3 B:LYS246 4.5 60.4 1.0 CG B:GLN199 4.6 63.0 1.0 OE2 B:GLU154 4.7 68.7 1.0 HB2 B:ASP197 4.7 50.1 1.0 CA B:ASP153 4.8 46.3 1.0 C B:LEU200 4.8 53.3 1.0 CG B:GLU154 4.8 56.0 1.0 NZ B:LYS246 4.8 50.3 1.0 N B:GLU154 4.9 38.8 1.0 H B:ILE198 4.9 56.3 1.0 CD2 B:LEU200 4.9 44.7 1.0 HB2 B:ASP153 4.9 54.6 1.0 HA B:GLU152 5.0 44.9 1.0 HA B:GLN199 5.0 67.2 1.0 O B:LEU200 5.0 48.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Rt-Phyr (RUTHE_01174)


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 Rt-Phyr (RUTHE_01174) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:67.7 occ:1.00 O C:HOH401 2.0 59.4 1.0 O C:GLN199 2.2 61.1 1.0 OD2 C:ASP197 2.4 60.2 1.0 OD1 C:ASP153 2.4 70.0 1.0 CG C:ASP153 3.1 69.3 1.0 OD2 C:ASP153 3.1 72.5 1.0 C C:GLN199 3.4 68.4 1.0 CG C:ASP197 3.4 61.7 1.0 HG3 C:GLU154 3.7 81.4 1.0 HB3 C:GLN199 3.7 89.1 1.0 HA C:LEU200 3.8 98.6 1.0 OD1 C:ASP197 3.8 66.6 1.0 HZ1 C:LYS246 3.8 79.1 1.0 H C:GLN199 4.0 72.2 1.0 OE2 C:GLU152 4.0 58.1 1.0 H C:ASP153 4.2 75.5 1.0 HD23 C:LEU200 4.2 68.1 1.0 OE2 C:GLU154 4.2 82.3 1.0 CA C:GLN199 4.3 65.3 1.0 CB C:GLN199 4.3 74.2 1.0 HB2 C:GLN199 4.3 89.1 1.0 N C:LEU200 4.3 73.4 1.0 CB C:ASP153 4.4 70.4 1.0 HZ3 C:LYS246 4.4 79.1 1.0 CA C:LEU200 4.5 82.0 1.0 HB3 C:ASP153 4.5 84.6 1.0 N C:GLN199 4.5 60.1 1.0 NZ C:LYS246 4.6 65.8 1.0 CG C:GLU154 4.6 67.8 1.0 CB C:ASP197 4.7 59.7 1.0 HB3 C:ASP197 4.8 71.7 1.0 H C:GLU154 4.9 73.3 1.0 CD C:GLU154 4.9 76.3 1.0 C C:LEU200 4.9 84.4 1.0 N C:ASP153 4.9 62.8 1.0 CD C:GLU152 5.0 66.2 1.0 HG2 C:GLU154 5.0 81.4 1.0

D.Swingle, L.Epstein, R.Aymon, E.A.Isiorho, R.R.Abzalimov, D.C.Favaro, K.H.Gardner. Variations in Kinase and Effector Signaling Logic in A Bacterial Two Component Signaling Network. J.Biol.Chem. 08534 2025.
ISSN: ESSN 1083-351X
PubMed: 40273983
DOI: 10.1016/J.JBC.2025.108534