Magnesium in PDB 5yxh: Structure of Rheb-Gdp

The structure of Structure of Rheb-Gdp, PDB code: 5yxh was solved by S.J.Mahoney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.80 / 2.04
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.166, 58.963, 64.345, 110.53, 90.03, 108.16
R / Rfree (%)	24.4 / 29.9

The binding sites of Magnesium atom in the Structure of Rheb-Gdp (pdb code 5yxh). 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 Rheb-Gdp, PDB code: 5yxh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Rheb-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rheb-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:35.2 occ:1.00 O A:HOH310 2.2 35.6 1.0 O A:HOH301 2.2 36.2 1.0 O A:HOH313 2.2 37.5 1.0 OG A:SER20 2.2 28.5 1.0 O1B A:GDP201 2.2 33.0 1.0 O A:HOH317 2.2 37.0 1.0 CB A:SER20 3.1 28.0 1.0 PB A:GDP201 3.2 31.7 1.0 O3B A:GDP201 3.4 32.9 1.0 O1A A:GDP201 3.7 34.4 1.0 CA A:PRO37 4.0 64.5 1.0 N A:SER20 4.0 27.4 1.0 CA A:SER20 4.1 27.8 1.0 O A:ASP36 4.2 64.4 1.0 O3A A:GDP201 4.3 33.2 1.0 PA A:GDP201 4.3 33.6 1.0 OD2 A:ASP60 4.3 35.1 1.0 O2B A:GDP201 4.3 31.5 1.0 CD2 A:TYR35 4.4 68.3 1.0 O2A A:GDP201 4.5 34.0 1.0 O A:ALA62 4.5 46.0 1.0 OD1 A:ASP60 4.6 35.6 1.0 N A:PRO37 4.7 65.2 1.0 C A:ASP36 4.7 66.8 1.0 CB A:PRO37 4.7 65.3 1.0 C A:PRO37 4.8 62.8 1.0 O A:THR61 4.8 37.3 1.0 CG A:ASP60 4.9 34.5 1.0 CE2 A:TYR35 4.9 68.8 1.0 O A:PRO37 5.0 60.0 1.0

Magnesium binding site 2 out of 4 in the Structure of Rheb-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rheb-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:37.0 occ:1.00 O B:HOH302 2.2 32.4 1.0 O B:HOH303 2.2 38.9 1.0 OG B:SER20 2.2 31.2 1.0 O B:HOH310 2.2 39.4 1.0 O3B B:GDP201 2.2 33.4 1.0 O B:HOH323 2.2 39.8 1.0 CB B:SER20 3.3 29.4 1.0 PB B:GDP201 3.3 33.9 1.0 O2B B:GDP201 3.4 32.0 1.0 CD2 B:TYR35 4.0 63.4 1.0 O2A B:GDP201 4.0 34.0 1.0 N B:SER20 4.2 28.7 1.0 O B:ASP36 4.2 69.8 1.0 CB B:TYR35 4.2 62.7 1.0 O3A B:GDP201 4.2 33.2 1.0 CA B:SER20 4.3 28.8 1.0 OD2 B:ASP60 4.3 31.6 1.0 O B:ALA62 4.3 40.1 1.0 O1B B:GDP201 4.5 33.4 1.0 CA B:PRO37 4.5 69.1 1.0 PA B:GDP201 4.5 32.6 1.0 CG B:TYR35 4.5 62.5 1.0 OD1 B:ASP60 4.6 32.5 1.0 C B:ASP36 4.7 70.3 1.0 O1A B:GDP201 4.7 33.5 1.0 O B:THR61 4.8 36.0 1.0 N B:PRO37 4.8 70.3 1.0 CG B:ASP60 4.9 31.8 1.0 CE2 B:TYR35 4.9 63.6 1.0 O B:TYR35 4.9 65.3 1.0 C B:TYR35 5.0 66.7 1.0

Magnesium binding site 3 out of 4 in the Structure of Rheb-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Rheb-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:36.7 occ:1.00 O C:HOH308 2.2 35.0 1.0 OG C:SER20 2.2 32.6 1.0 O C:HOH312 2.2 38.3 1.0 O C:HOH303 2.2 36.6 1.0 O1B C:GDP201 2.2 38.1 1.0 O C:HOH322 2.2 38.8 1.0 CB C:SER20 3.2 31.2 1.0 PB C:GDP201 3.3 37.9 1.0 O3B C:GDP201 3.5 38.2 1.0 N C:SER20 4.0 31.9 1.0 CD1 C:TYR35 4.0 79.9 1.0 O1A C:GDP201 4.0 35.2 1.0 OD2 C:ASP60 4.1 34.6 1.0 CA C:PRO37 4.1 78.5 1.0 CA C:SER20 4.1 30.9 1.0 CE1 C:TYR35 4.2 81.7 1.0 O C:ASP36 4.3 77.6 1.0 O3A C:GDP201 4.3 36.6 1.0 OD1 C:ASP60 4.4 34.9 1.0 O2B C:GDP201 4.4 37.3 1.0 PA C:GDP201 4.5 35.3 1.0 O C:ALA62 4.6 48.6 1.0 CG C:ASP60 4.6 34.5 1.0 CB C:PRO37 4.6 79.4 1.0 O2A C:GDP201 4.7 36.4 1.0 O C:THR61 4.8 37.4 1.0 N C:PRO37 4.8 78.7 1.0 C C:ASP36 4.8 79.1 1.0

Magnesium binding site 4 out of 4 in the Structure of Rheb-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Rheb-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:39.4 occ:1.00 OG D:SER20 2.2 33.6 1.0 O3B D:GDP201 2.2 36.3 1.0 O D:HOH311 2.2 42.8 1.0 O D:HOH305 2.2 36.8 1.0 O D:HOH301 2.2 36.4 1.0 O D:HOH330 2.2 41.9 1.0 CB D:SER20 3.2 33.0 1.0 PB D:GDP201 3.3 37.1 1.0 O2B D:GDP201 3.6 37.4 1.0 N D:SER20 3.9 32.4 1.0 OD2 D:ASP60 3.9 40.4 1.0 OD1 D:ASP60 4.1 40.0 1.0 CA D:SER20 4.1 31.9 1.0 O D:ASP36 4.2 84.4 1.0 CD2 D:TYR35 4.2 79.9 1.0 O2A D:GDP201 4.2 37.7 1.0 O D:ALA62 4.3 46.0 1.0 O1B D:GDP201 4.3 35.2 1.0 CE2 D:TYR35 4.4 80.7 1.0 O3A D:GDP201 4.4 36.3 1.0 CG D:ASP60 4.4 40.5 1.0 O D:THR61 4.5 38.4 1.0 PA D:GDP201 4.6 39.2 1.0 O1A D:GDP201 4.8 38.0 1.0 CB D:LYS19 4.8 30.7 1.0 CE D:LYS19 4.9 31.3 1.0 O D:PRO37 4.9 78.4 1.0 CA D:PRO37 4.9 81.6 1.0 C D:LYS19 5.0 31.6 1.0

S.J.Mahoney, S.Narayan, L.Molz, L.A.Berstler, S.A.Kang, G.P.Vlasuk, E.Saiah. A Small Molecule Inhibitor of Rheb Selectively Targets MTORC1 Signaling. Nat Commun V. 9 548 2018.
ISSN: ESSN 2041-1723
PubMed: 29416044
DOI: 10.1038/S41467-018-03035-Z