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Sodium in PDB 7dph: H-Ras Q61H in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control

Enzymatic activity of H-Ras Q61H in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control

All present enzymatic activity of H-Ras Q61H in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control:
3.6.5.2;

Protein crystallography data

The structure of H-Ras Q61H in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control, PDB code: 7dph was solved by H.Taniguchi, S.Matsumoto, 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) 23.21 / 1.54
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 91.769, 91.769, 121.268, 90, 90, 120
R / Rfree (%) 19.2 / 20.2

Other elements in 7dph:

The structure of H-Ras Q61H in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the H-Ras Q61H in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control (pdb code 7dph). 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 Q61H in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control, PDB code: 7dph:

Sodium binding site 1 out of 1 in 7dph

Go back to Sodium Binding Sites List in 7dph
Sodium binding site 1 out of 1 in the H-Ras Q61H 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 Q61H in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:20.9
occ:1.00
 O A:HOH346 2.2 25.4 1.0
O A:ASP107 2.3 24.9 1.0
O A:TYR137 2.5 17.9 1.0
O A:HOH306 2.6 26.7 1.0
NH2 A:ARG97 2.9 23.7 0.5
C A:ASP107 3.4 25.1 1.0
CZ A:ARG97 3.5 22.9 0.5
C A:TYR137 3.7 17.3 1.0
NH1 A:ARG97 3.7 24.1 0.5
N A:ASP108 4.2 24.6 0.5
N A:ASP108 4.2 24.4 0.5
CA A:ASP108 4.2 24.0 0.5
CA A:ASP108 4.2 24.3 0.5
NH2 A:ARG97 4.3 21.6 0.5
CA A:ASP107 4.4 26.5 1.0
NE A:ARG97 4.4 21.9 0.5
CA A:TYR137 4.4 17.6 1.0
OD1 A:ASP108 4.4 25.7 0.5
N A:VAL109 4.4 21.2 1.0
CG2 A:ILE139 4.6 14.2 1.0
CB A:TYR137 4.7 17.7 1.0
O A:HOH394 4.7 22.5 1.0
CB A:ASP107 4.7 28.9 1.0
N A:GLY138 4.8 16.7 1.0
O A:VAL109 4.8 16.9 1.0
C A:ASP108 4.9 23.0 0.5
C A:ASP108 4.9 22.9 0.5

Reference:

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
Page generated: Tue Oct 8 16:37:54 2024

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