Magnesium in PDB 7jii: Hras A59E Gdp

The structure of Hras A59E Gdp, PDB code: 7jii was solved by C.W.Johnson, K.M.Haigis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.14 / 1.53
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.593, 37.946, 56.254, 107.36, 107.19, 95.32
R / Rfree (%)	15.8 / 20.3

The structure of Hras A59E Gdp also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Hras A59E Gdp (pdb code 7jii). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hras A59E Gdp, PDB code: 7jii:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hras A59E Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hras A59E Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:18.0 occ:1.00 OG A:SER17 2.0 15.8 1.0 O A:HOH336 2.1 19.2 1.0 O A:HOH333 2.1 20.2 1.0 O2B A:GDP201 2.1 14.3 1.0 O A:HOH347 2.2 17.5 1.0 O A:HOH321 2.2 21.7 1.0 CB A:SER17 3.1 14.4 1.0 PB A:GDP201 3.4 15.4 1.0 O1B A:GDP201 3.6 16.4 1.0 N A:SER17 3.8 11.9 1.0 OD2 A:ASP57 3.9 20.0 1.0 CA A:SER17 4.0 12.6 1.0 OD1 A:ASP57 4.1 18.0 1.0 O1A A:GDP201 4.2 15.8 1.0 O A:HOH308 4.2 30.9 1.0 CG A:PRO34 4.2 33.8 1.0 OE2 A:GLU59 4.3 41.9 1.0 O A:HOH348 4.3 34.4 1.0 O3B A:GDP201 4.4 16.3 1.0 CG A:ASP57 4.4 17.4 1.0 OE1 A:GLU59 4.4 37.0 1.0 CD A:GLU59 4.4 37.4 1.0 CD A:PRO34 4.5 32.4 1.0 O3A A:GDP201 4.5 15.5 1.0 O A:THR58 4.6 23.6 1.0 PA A:GDP201 4.7 15.8 1.0 O A:HOH309 4.7 37.9 1.0 O A:HOH378 4.7 23.7 1.0 O2A A:GDP201 4.7 15.8 1.0 CE A:LYS16 4.9 15.2 1.0 CB A:LYS16 4.9 14.1 1.0 C A:LYS16 4.9 12.8 1.0 O A:HOH415 5.0 19.2 1.0 NZ A:LYS16 5.0 15.7 1.0

Magnesium binding site 2 out of 2 in the Hras A59E Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hras A59E Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:15.8 occ:1.00 O B:HOH365 2.1 18.8 1.0 O2B B:GDP201 2.1 15.0 1.0 O B:HOH327 2.1 18.4 1.0 O B:HOH411 2.1 19.0 1.0 OG B:SER17 2.1 15.5 1.0 O B:HOH316 2.2 17.3 1.0 CB B:SER17 3.2 13.9 1.0 PB B:GDP201 3.3 14.8 1.0 O3B B:GDP201 3.5 15.9 1.0 N B:SER17 3.9 13.5 1.0 OD2 B:ASP57 4.1 18.9 1.0 CA B:SER17 4.1 14.4 1.0 O2A B:GDP201 4.2 16.6 1.0 O B:HOH421 4.2 27.1 1.0 OD1 B:ASP57 4.3 18.7 1.0 OE2 B:GLU59 4.3 43.2 1.0 O1B B:GDP201 4.3 14.2 1.0 CD1 B:TYR32 4.3 26.0 1.0 O3A B:GDP201 4.4 17.5 1.0 O B:HOH392 4.4 31.6 1.0 OE1 B:GLU59 4.5 42.2 1.0 O B:THR58 4.5 20.8 1.0 CG B:ASP57 4.6 18.9 1.0 PA B:GDP201 4.6 16.0 1.0 CE1 B:TYR32 4.7 26.7 1.0 O1A B:GDP201 4.7 15.0 1.0 O B:HOH318 4.7 25.4 1.0 CD B:GLU59 4.8 37.3 1.0 O B:HOH372 4.9 26.0 1.0 CB B:LYS16 4.9 14.4 1.0 CE B:LYS16 5.0 16.4 1.0 C B:LYS16 5.0 13.3 1.0

C.W.Johnson, H.S.Seo, E.M.Terrell, M.H.Yang, F.Kleinjan, T.Gebregiworgis, G.M.C.Gasmi-Seabrook, E.A.Geffken, J.Lakhani, K.Song, P.Bashyal, O.Popow, J.A.Paulo, A.Liu, C.Mattos, C.B.Marshall, M.Ikura, D.K.Morrison, S.Dhe-Paganon, K.M.Haigis. Regulation of Gtpase Function By Autophosphorylation. Mol.Cell V. 82 950 2022.
ISSN: ISSN 1097-2765
PubMed: 35202574
DOI: 10.1016/J.MOLCEL.2022.02.011