Sodium 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:

Magnesium

(Mg)

2 atoms

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

Sodium 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 Sodium with other atoms in the Na binding site number 1 of Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:25.6 occ:1.00 O B:HOH353 2.1 17.5 1.0 O A:HOH329 2.1 30.1 1.0 OD1 A:ASP33 2.1 18.8 1.0 O B:HOH305 2.2 18.5 1.0 O A:HOH325 2.2 20.7 1.0 O A:HOH330 2.4 32.7 1.0 CG A:ASP33 3.1 17.8 1.0 OD2 A:ASP33 3.4 29.4 1.0 OE2 B:GLU125 3.8 29.2 1.0 OE1 B:GLU125 3.8 16.9 1.0 O A:PRO34 4.1 10.4 1.0 CD B:GLU125 4.2 24.7 1.0 HD2 A:PRO34 4.3 22.5 1.0 CB A:ASP33 4.5 12.1 1.0 HA A:ASP33 4.5 15.3 1.0 C A:ASP33 4.7 9.5 1.0 CA A:ASP33 4.8 12.8 1.0 N A:PRO34 4.8 12.2 1.0 HB2 A:ASP33 4.9 14.5 1.0 O B:HOH303 4.9 23.2 1.0 CD A:PRO34 5.0 18.8 1.0

Sodium 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 Sodium with other atoms in the Na binding site number 2 of Choanoflagellate Salpingoeca Rosetta Ras with Gmp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:19.5 occ:1.00 OD1 B:ASP33 2.0 19.1 1.0 O B:HOH328 2.0 22.5 1.0 O B:HOH315 2.1 22.7 1.0 O B:HOH302 2.1 20.8 1.0 CG B:ASP33 2.9 18.7 1.0 OD2 B:ASP33 3.1 25.9 1.0 O B:PRO34 4.0 14.6 1.0 O A:HOH382 4.2 24.7 1.0 CB B:ASP33 4.3 13.3 1.0 HD2 B:PRO34 4.4 19.0 1.0 HA B:ASP33 4.4 16.8 1.0 CA B:ASP33 4.7 14.0 1.0 C B:ASP33 4.8 20.3 1.0 HB3 B:ASP33 4.8 15.9 1.0 HB2 B:ASP33 4.8 15.9 1.0 N B:PRO34 4.9 16.7 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