Magnesium in PDB 5b2z: H-Ras Wt in Complex with Gppnhp (State 2*) Before Structural Transition By Humidity Control

The structure of H-Ras Wt in Complex with Gppnhp (State 2*) Before Structural Transition By Humidity Control, PDB code: 5b2z 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)	25.40 / 1.56
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	87.974, 87.974, 132.966, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 17.8

The structure of H-Ras Wt in Complex with Gppnhp (State 2*) Before Structural Transition By Humidity Control also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the H-Ras Wt in Complex with Gppnhp (State 2*) Before Structural Transition By Humidity Control (pdb code 5b2z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the H-Ras Wt in Complex with Gppnhp (State 2*) Before Structural Transition By Humidity Control, PDB code: 5b2z:

Magnesium binding site 1 out of 1 in the H-Ras Wt in Complex with Gppnhp (State 2*) Before Structural Transition By Humidity Control


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of H-Ras Wt in Complex with Gppnhp (State 2*) Before Structural Transition By Humidity Control within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:9.9 occ:1.00 O2G A:GNP201 2.0 12.1 1.0 O A:HOH342 2.1 10.8 1.0 OG1 A:THR35 2.1 10.7 1.0 OG A:SER17 2.1 9.2 1.0 O A:HOH336 2.1 9.6 1.0 O2B A:GNP201 2.1 9.2 1.0 CB A:THR35 3.1 10.3 1.0 PG A:GNP201 3.2 12.2 1.0 CB A:SER17 3.2 8.5 1.0 PB A:GNP201 3.3 10.1 1.0 N3B A:GNP201 3.4 9.8 1.0 N A:THR35 3.8 11.1 1.0 N A:SER17 3.9 8.5 1.0 O1G A:GNP201 4.0 13.0 1.0 OD2 A:ASP57 4.1 11.0 1.0 CA A:THR35 4.1 12.1 1.0 O A:HOH354 4.1 13.7 1.0 CA A:SER17 4.1 8.3 1.0 O2A A:GNP201 4.1 10.1 1.0 CG2 A:THR35 4.1 11.1 1.0 OD1 A:ASP57 4.2 10.3 1.0 O3A A:GNP201 4.3 9.1 1.0 O1B A:GNP201 4.3 9.6 1.0 O3G A:GNP201 4.3 12.6 1.0 O A:ASP33 4.4 11.5 1.0 CG A:ASP57 4.5 10.7 1.0 PA A:GNP201 4.5 9.7 1.0 O A:THR58 4.6 11.8 1.0 O1A A:GNP201 4.7 9.3 1.0 C A:PRO34 4.8 12.7 1.0 CB A:LYS16 4.8 8.8 1.0 C A:LYS16 5.0 9.1 1.0

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