Magnesium in PDB 5wdr: Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp

All present enzymatic activity of Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp:
3.6.5.2;

The structure of Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp, PDB code: 5wdr 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)	34.26 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.562, 119.106, 38.570, 90.00, 117.34, 90.00
R / Rfree (%)	22.9 / 28

The structure of Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp (pdb code 5wdr). 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 Gmp-Pnp, PDB code: 5wdr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp


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 Gmp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:12.6 occ:1.00 O1B A:GNP203 1.9 9.2 1.0 O1G A:GNP203 2.0 11.6 1.0 O A:HOH327 2.0 13.5 1.0 OG A:SER17 2.1 13.5 1.0 OG1 A:THR35 2.1 13.2 1.0 O A:HOH326 2.2 17.0 1.0 HB A:THR35 2.9 18.6 1.0 CB A:THR35 3.1 15.5 1.0 PG A:GNP203 3.1 11.7 1.0 H A:THR35 3.1 15.2 1.0 PB A:GNP203 3.2 11.4 1.0 HB2 A:SER17 3.2 13.1 1.0 H A:SER17 3.2 11.2 1.0 CB A:SER17 3.2 10.9 1.0 N3B A:GNP203 3.4 14.5 1.0 N A:THR35 3.7 12.7 1.0 HB2 A:LYS16 3.7 16.4 1.0 N A:SER17 3.8 9.3 1.0 HB3 A:SER17 3.9 13.1 1.0 O2G A:GNP203 4.0 12.5 1.0 OD2 A:ASP57 4.0 14.0 1.0 CA A:THR35 4.0 12.5 1.0 HE2 A:LYS16 4.0 15.7 1.0 CA A:SER17 4.1 11.8 1.0 HA A:PRO34 4.1 17.3 1.0 OD1 A:ASP57 4.1 15.9 1.0 O A:HOH307 4.1 17.8 1.0 O2A A:GNP203 4.1 9.9 1.0 HG21 A:THR35 4.2 13.6 1.0 CG2 A:THR35 4.2 11.3 1.0 O3A A:GNP203 4.2 10.8 1.0 HNB3 A:GNP203 4.3 17.4 1.0 O2B A:GNP203 4.3 9.8 1.0 HA A:SER17 4.4 14.1 1.0 O3G A:GNP203 4.4 17.8 1.0 CG A:ASP57 4.4 17.1 1.0 O A:ASP33 4.4 14.8 1.0 O A:THR58 4.5 14.6 1.0 HE1 A:TYR32 4.5 17.2 1.0 HA A:THR35 4.5 15.0 1.0 PA A:GNP203 4.5 9.3 1.0 O1A A:GNP203 4.5 9.1 1.0 CB A:LYS16 4.6 13.7 1.0 HB3 A:LYS16 4.6 16.4 1.0 C A:PRO34 4.6 11.9 1.0 HG23 A:THR35 4.7 13.6 1.0 HZ3 A:LYS16 4.7 12.2 1.0 HZ1 A:LYS16 4.8 12.2 1.0 CA A:PRO34 4.8 14.4 1.0 CE A:LYS16 4.9 13.1 1.0 C A:LYS16 4.9 8.7 1.0 HG22 A:THR35 4.9 13.6 1.0

Magnesium binding site 2 out of 2 in the Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp


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 Gmp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:9.8 occ:1.00 O1B B:GNP203 1.9 10.6 1.0 O2G B:GNP203 2.0 16.2 1.0 OG B:SER17 2.1 14.4 1.0 O B:HOH340 2.1 12.8 1.0 OG1 B:THR35 2.1 14.8 1.0 O B:HOH322 2.2 12.2 1.0 HB B:THR35 2.9 19.8 1.0 CB B:THR35 3.1 16.5 1.0 HB2 B:SER17 3.1 16.6 1.0 CB B:SER17 3.2 13.9 1.0 PB B:GNP203 3.2 12.5 1.0 PG B:GNP203 3.2 15.0 1.0 H B:SER17 3.3 13.8 1.0 H B:THR35 3.4 15.7 1.0 N3B B:GNP203 3.5 8.3 1.0 N B:THR35 3.8 13.1 1.0 HB3 B:SER17 3.8 16.6 1.0 N B:SER17 3.9 11.5 1.0 HB2 B:LYS16 3.9 15.8 1.0 OD2 B:ASP57 4.0 17.3 1.0 O1G B:GNP203 4.0 16.7 1.0 HG21 B:THR35 4.0 20.3 1.0 CA B:THR35 4.1 18.9 1.0 CA B:SER17 4.1 12.1 1.0 HE2 B:LYS16 4.1 18.3 1.0 O2B B:GNP203 4.2 9.7 1.0 CG2 B:THR35 4.2 16.9 1.0 O1A B:GNP203 4.2 10.6 1.0 OD1 B:ASP57 4.2 14.9 1.0 HA B:PRO34 4.3 14.7 1.0 O3A B:GNP203 4.3 10.4 1.0 HNB3 B:GNP203 4.3 9.9 1.0 O3G B:GNP203 4.4 13.2 1.0 O B:HOH321 4.4 17.0 1.0 O B:ASP33 4.4 14.3 1.0 HA B:SER17 4.4 14.5 1.0 CG B:ASP57 4.4 18.6 1.0 HE1 B:TYR32 4.5 18.2 1.0 PA B:GNP203 4.5 10.0 1.0 O B:THR58 4.5 11.9 1.0 HA B:THR35 4.5 22.6 1.0 HZ1 B:LYS16 4.5 13.4 1.0 O2A B:GNP203 4.6 12.2 1.0 HG23 B:THR35 4.6 20.3 1.0 C B:PRO34 4.7 16.3 1.0 HZ3 B:LYS16 4.7 13.4 1.0 CB B:LYS16 4.8 13.1 1.0 HG22 B:THR35 4.9 20.3 1.0 NZ B:LYS16 4.9 11.2 1.0 CE B:LYS16 4.9 15.3 1.0 CA B:PRO34 4.9 12.2 1.0 C B:LYS16 5.0 12.6 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