Calcium 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:

Magnesium

(Mg)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the H-Ras Wt in Complex with Gppnhp (State 2*) Before Structural Transition By Humidity Control, PDB code: 5b2z:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca202 b:10.8 occ:1.00 O A:PHE28 2.3 10.6 1.0 OD1 A:ASP30 2.3 12.2 1.0 O A:HOH434 2.4 15.6 1.0 CG A:ASP30 3.5 12.5 1.0 C A:PHE28 3.5 10.6 1.0 N A:ASP30 4.0 9.9 1.0 O A:HOH359 4.3 23.9 1.0 CA A:VAL29 4.4 10.2 1.0 N A:VAL29 4.4 9.7 1.0 CB A:ASP30 4.4 11.6 1.0 O A:HOH411 4.4 18.6 1.0 OD2 A:ASP30 4.5 14.4 1.0 CA A:PHE28 4.6 9.8 1.0 O A:HOH441 4.6 27.6 1.0 C A:VAL29 4.6 10.6 1.0 N A:PHE28 4.7 10.6 1.0 CB A:PHE28 4.8 10.6 1.0 CA A:ASP30 4.8 12.2 1.0 CD2 A:PHE28 5.0 11.1 1.0

Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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:Ca204 b:19.1 occ:0.50 O A:ARG102 2.2 15.7 0.5 OD1 A:ASP105 2.2 24.9 1.0 O A:ARG102 2.3 14.0 0.5 O A:HOH415 2.4 23.5 0.5 OD2 A:ASP105 2.4 29.1 1.0 CG A:ASP105 2.7 22.2 1.0 C A:ARG102 3.4 16.3 0.5 C A:ARG102 3.4 16.5 0.5 CB A:ASP105 4.1 22.6 1.0 CA A:ARG102 4.2 15.1 0.5 N A:VAL103 4.3 14.9 1.0 CA A:VAL103 4.3 15.3 1.0 O A:HOH322 4.3 33.3 1.0 CA A:ARG102 4.3 14.5 0.5 N A:ASP105 4.4 18.3 1.0 C A:VAL103 4.5 16.4 1.0 O A:VAL103 4.5 19.3 1.0 CB A:ARG102 4.5 17.2 0.5 CA A:ASP105 4.6 19.4 1.0 CG A:ARG102 4.8 18.9 0.5 NH1 A:ARG73 4.8 34.8 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