Magnesium in PDB 3sea: Structure of Rheb-Y35A Mutant in Gdp- and Gmppnp-Bound Forms

The structure of Structure of Rheb-Y35A Mutant in Gdp- and Gmppnp-Bound Forms, PDB code: 3sea was solved by M.T.Mazhab-Jafari, C.B.Marshall, N.Ishiyama, S.Vuk, M.Ikura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.92 / 2.00
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.247, 69.873, 79.195, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 21.4

The binding sites of Magnesium atom in the Structure of Rheb-Y35A Mutant in Gdp- and Gmppnp-Bound Forms (pdb code 3sea). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Rheb-Y35A Mutant in Gdp- and Gmppnp-Bound Forms, PDB code: 3sea:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Rheb-Y35A Mutant in Gdp- and Gmppnp-Bound Forms


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-Y35A Mutant in Gdp- and Gmppnp-Bound Forms within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:21.8 occ:1.00 O A:HOH170 2.1 17.2 1.0 O A:HOH176 2.1 17.8 1.0 OG A:SER20 2.1 21.8 1.0 O A:HOH172 2.2 22.9 1.0 O3B A:GDP201 2.2 16.1 1.0 O A:HOH197 2.4 16.9 1.0 CB A:SER20 3.1 13.8 1.0 PB A:GDP201 3.4 17.0 1.0 O1B A:GDP201 3.6 18.3 1.0 N A:SER20 3.8 19.6 1.0 OD2 A:ASP60 3.9 19.6 1.0 CA A:SER20 4.0 23.8 1.0 OD1 A:ASP60 4.1 17.8 1.0 O1A A:GDP201 4.1 18.4 1.0 O A:ASP36 4.2 31.1 1.0 O2B A:GDP201 4.4 15.6 1.0 CG A:ASP60 4.4 24.1 1.0 O A:THR61 4.5 20.5 1.0 O3A A:GDP201 4.5 19.8 1.0 PA A:GDP201 4.7 17.2 1.0 O2A A:GDP201 4.7 16.2 1.0 CE A:LYS19 4.7 17.1 1.0 CB A:LYS19 4.7 12.5 1.0 O A:ALA35 4.8 38.6 1.0 CA A:PRO37 4.8 36.5 1.0 O A:PRO37 4.8 38.5 1.0 C A:LYS19 4.9 13.6 1.0 NZ A:LYS19 4.9 16.1 1.0 CB A:ALA35 5.0 35.6 1.0

Magnesium binding site 2 out of 2 in the Structure of Rheb-Y35A Mutant in Gdp- and Gmppnp-Bound Forms


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-Y35A Mutant in Gdp- and Gmppnp-Bound Forms within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg178 b:26.7 occ:1.00 O B:HOH262 2.1 18.8 1.0 O2G B:GNP179 2.1 18.7 1.0 OG1 B:THR38 2.2 26.8 1.0 O2B B:GNP179 2.2 20.5 1.0 OG B:SER20 2.2 19.6 1.0 O B:HOH174 2.3 20.4 1.0 CB B:THR38 3.1 24.9 1.0 CB B:SER20 3.2 18.7 1.0 PG B:GNP179 3.3 22.1 1.0 PB B:GNP179 3.3 18.5 1.0 N3B B:GNP179 3.4 13.7 1.0 N B:THR38 3.7 25.4 1.0 N B:SER20 3.9 18.9 1.0 CA B:THR38 3.9 28.1 1.0 OD2 B:ASP60 4.0 21.3 1.0 CA B:SER20 4.1 21.1 1.0 OXT B:ACT1 4.2 51.4 1.0 OD1 B:ASP60 4.2 20.5 1.0 O3G B:GNP179 4.2 18.3 1.0 O2A B:GNP179 4.3 18.2 1.0 O B:ASP36 4.3 37.5 1.0 O1B B:GNP179 4.3 19.1 1.0 CG2 B:THR38 4.3 22.6 1.0 O B:THR61 4.3 21.5 1.0 O1G B:GNP179 4.3 21.6 1.0 O B:HOH267 4.4 34.6 1.0 O3A B:GNP179 4.4 22.1 1.0 CG B:ASP60 4.5 26.6 1.0 PA B:GNP179 4.7 22.0 1.0 C B:PRO37 4.7 33.1 1.0 CE B:LYS19 4.8 20.0 1.0 O1A B:GNP179 4.8 22.3 1.0 CB B:LYS19 4.8 14.9 1.0 C B:ACT1 4.9 55.0 1.0 C B:LYS19 5.0 18.4 1.0 CH3 B:ACT1 5.0 51.1 1.0 NZ B:LYS19 5.0 20.2 1.0

M.T.Mazhab-Jafari, C.B.Marshall, N.Ishiyama, J.Ho, V.Di Palma, V.Stambolic, M.Ikura. An Autoinhibited Noncanonical Mechanism of Gtp Hydrolysis By Rheb Maintains MTORC1 Homeostasis. Structure V. 20 1528 2012.
ISSN: ISSN 0969-2126
PubMed: 22819219
DOI: 10.1016/J.STR.2012.06.013