Magnesium in PDB 5wds: Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound

All present enzymatic activity of Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound:
3.6.5.2;

The structure of Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound, PDB code: 5wds was solved by Y.Kondo, C.L.Gee, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.53 / 1.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.222, 67.222, 184.679, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.9

The binding sites of Magnesium atom in the Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound (pdb code 5wds). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound, PDB code: 5wds:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:38.7 occ:1.00 O A:HOH304 2.0 42.7 1.0 O A:HOH316 2.0 38.9 1.0 O3B A:GDP201 2.1 44.6 1.0 O A:HOH341 2.1 44.6 1.0 OG A:SER17 2.2 45.5 1.0 O A:HOH306 2.4 54.2 1.0 PB A:GDP201 3.3 41.0 1.0 CB A:SER17 3.3 42.7 1.0 O1B A:GDP201 3.4 41.7 1.0 N A:SER17 3.9 34.5 1.0 O1A A:GDP201 4.1 46.9 1.0 OD2 A:ASP57 4.1 50.9 1.0 O2B A:GDP201 4.1 42.8 1.0 CA A:SER17 4.1 43.9 1.0 OD1 A:ASP57 4.2 52.4 1.0 O A:THR58 4.3 46.0 1.0 O A:ASP33 4.4 59.3 1.0 CB A:ALA59 4.4 54.0 1.0 O3A A:GDP201 4.5 38.1 1.0 O A:PRO34 4.5 55.8 1.0 O A:ILE36 4.6 53.6 1.0 CG A:ASP57 4.6 52.8 1.0 CA A:PRO34 4.6 55.9 1.0 PA A:GDP201 4.7 43.0 1.0 CD2 A:TYR32 4.7 55.2 1.0 CB A:LYS16 4.8 32.5 1.0 O2A A:GDP201 4.8 44.6 1.0 C A:PRO34 4.8 55.9 1.0 NZ A:LYS16 4.8 40.9 1.0 CE A:LYS16 4.9 40.0 1.0 C A:LYS16 4.9 37.7 1.0 CA A:ALA59 5.0 53.5 1.0

Magnesium binding site 2 out of 2 in the Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Choanoflagellate Salpingoeca Rosetta Ras with Gdp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:39.9 occ:1.00 O B:HOH309 2.0 43.8 1.0 O B:HOH338 2.0 46.1 1.0 O B:HOH317 2.1 42.0 1.0 OG B:SER17 2.1 39.8 1.0 O1B B:GDP201 2.1 38.5 1.0 O B:HOH337 2.3 44.4 1.0 CB B:SER17 3.2 34.8 1.0 PB B:GDP201 3.3 39.4 1.0 O2B B:GDP201 3.4 39.9 1.0 O2A B:GDP201 3.8 45.7 1.0 N B:SER17 3.9 34.4 1.0 CA B:SER17 4.2 35.6 1.0 O3B B:GDP201 4.2 34.9 1.0 OD2 B:ASP57 4.3 45.3 1.0 O B:ASP33 4.3 54.9 1.0 O3A B:GDP201 4.3 32.9 1.0 PA B:GDP201 4.4 41.7 1.0 CA B:PRO34 4.5 54.4 1.0 OD1 B:ASP57 4.5 47.1 1.0 O B:ILE36 4.5 47.1 1.0 O B:THR58 4.5 43.5 1.0 CB B:ALA59 4.5 52.9 1.0 O B:PRO34 4.6 50.5 1.0 O1A B:GDP201 4.6 41.0 1.0 CD2 B:TYR32 4.6 51.8 1.0 C B:PRO34 4.7 54.1 1.0 CG B:ASP57 4.8 49.0 1.0 O B:HOH321 4.9 46.1 1.0 CB B:LYS16 5.0 31.0 1.0 NZ B:LYS16 5.0 38.2 1.0

P.Bandaru, N.H.Shah, M.Bhattacharyya, J.P.Barton, Y.Kondo, J.C.Cofsky, C.L.Gee, A.K.Chakraborty, T.Kortemme, R.Ranganathan, J.Kuriyan. Deconstruction of the Ras Switching Cycle Through Saturation Mutagenesis. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28686159
DOI: 10.7554/ELIFE.27810