Sodium in PDB 5b30: H-Ras Wt in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control

The structure of H-Ras Wt in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control, PDB code: 5b30 was solved by T.Kumasaka, N.Miyano, S.Baba, S.Matsumoto, T.Kataoka, F.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.36 / 1.60
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	91.791, 91.791, 121.417, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 19.6

The structure of H-Ras Wt in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the H-Ras Wt in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control (pdb code 5b30). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the H-Ras Wt in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control, PDB code: 5b30:

Sodium binding site 1 out of 1 in the H-Ras Wt in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of H-Ras Wt in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:20.2 occ:1.00 NH2 A:ARG97 2.2 14.8 0.5 O A:ASP107 2.2 21.6 1.0 O A:HOH349 2.3 24.0 1.0 O A:HOH403 2.3 37.3 1.0 O A:TYR137 2.4 19.8 1.0 CZ A:ARG97 3.0 13.4 0.5 NH1 A:ARG97 3.1 19.5 0.5 C A:ASP107 3.4 19.1 1.0 C A:TYR137 3.6 18.5 1.0 N A:ASP108 4.2 19.2 0.5 CA A:ASP108 4.2 20.6 0.5 N A:ASP108 4.2 19.4 0.5 NE A:ARG97 4.2 17.1 0.5 CA A:ASP108 4.2 21.3 0.5 NH2 A:ARG97 4.3 28.6 0.5 CA A:ASP107 4.3 21.8 1.0 CA A:TYR137 4.4 18.5 1.0 N A:VAL109 4.5 20.4 1.0 OD1 A:ASP108 4.5 32.1 0.5 O A:HOH315 4.5 22.6 1.0 CB A:ASP107 4.6 30.2 1.0 N A:GLY138 4.6 17.3 1.0 CG2 A:ILE139 4.6 16.4 1.0 CB A:TYR137 4.7 18.5 1.0 O A:HOH438 4.7 20.9 1.0 C A:ASP108 4.8 21.7 0.5 CA A:GLY138 4.9 17.9 1.0 O A:VAL109 4.9 16.1 1.0 NE A:ARG97 4.9 19.8 0.5 C A:ASP108 4.9 20.5 0.5

S.Matsumoto, N.Miyano, S.Baba, J.Liao, T.Kawamura, C.Tsuda, A.Takeda, M.Yamamoto, T.Kumasaka, T.Kataoka, F.Shima. Molecular Mechanism For Conformational Dynamics of Ras-Gtp Elucidated From in-Situ Structural Transition in Crystal Sci Rep V. 6 25931 2016.
ISSN: ESSN 2045-2322
PubMed: 27180801
DOI: 10.1038/SREP25931