Magnesium in PDB 7dpj: H-Ras Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control

All present enzymatic activity of H-Ras Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control:
3.6.5.2;

The structure of H-Ras Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control, PDB code: 7dpj was solved by H.Taniguchi, S.Matsumoto, R.Miyamoto, T.Kawamura, T.Kumasaka, T.Kataoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 1.98
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	91.844, 91.844, 121.413, 90, 90, 120
R / Rfree (%)	19 / 22.1

The structure of H-Ras Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the H-Ras Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control (pdb code 7dpj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the H-Ras Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control, PDB code: 7dpj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the H-Ras Q61L in Complex with Gppnhp (State 1) After 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 Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:14.9 occ:1.00 O2G A:GNP206 2.0 22.6 1.0 O A:HOH318 2.1 20.8 1.0 O A:HOH313 2.2 22.5 1.0 OG A:SER17 2.2 17.5 1.0 O2B A:GNP206 2.2 18.9 1.0 O A:HOH357 2.3 21.5 1.0 CB A:SER17 3.3 17.2 1.0 PG A:GNP206 3.3 22.2 1.0 PB A:GNP206 3.4 19.9 1.0 N3B A:GNP206 3.7 20.0 1.0 N A:SER17 4.1 17.8 1.0 OD2 A:ASP57 4.1 24.4 1.0 O2A A:GNP206 4.1 19.4 1.0 O3G A:GNP206 4.2 22.3 1.0 CA A:SER17 4.3 18.3 1.0 OD1 A:ASP57 4.3 25.5 1.0 O1G A:GNP206 4.4 21.2 1.0 O A:HOH351 4.5 39.4 1.0 O1B A:GNP206 4.5 18.9 1.0 O3A A:GNP206 4.5 18.9 1.0 CG A:ASP57 4.6 26.3 1.0 PA A:GNP206 4.7 20.9 1.0 O1A A:GNP206 4.8 18.1 1.0 O A:HOH303 4.8 19.4 1.0 O A:THR58 4.8 28.5 1.0 CD1 A:ILE36 4.9 31.3 1.0

Magnesium binding site 2 out of 2 in the H-Ras Q61L in Complex with Gppnhp (State 1) After 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 2 of H-Ras Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:5.8 occ:0.33 O A:HOH335 2.2 19.9 1.0 O A:HOH345 2.4 25.6 1.0 O A:THR124 4.3 16.6 1.0 OE2 A:GLU126 4.3 35.6 1.0 O A:HOH323 4.4 19.9 1.0 OE1 A:GLN129 4.9 20.1 1.0

S.Matsumoto, H.Taniguchi-Tamura, M.Araki, T.Kawamura, R.Miyamoto, C.Tsuda, F.Shima, T.Kumasaka, Y.Okuno, T.Kataoka. Oncogenic Mutations Q61L and Q61H Confer Active Form-Like Structural Features to the Inactive State (State 1) Conformation of H-Ras Protein. Biochem.Biophys.Res.Commun. V. 565 85 2021.
ISSN: ESSN 1090-2104
PubMed: 34102474
DOI: 10.1016/J.BBRC.2021.05.084