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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7dpj:

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

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the H-Ras Q61L in Complex with Gppnhp (State 1) After Structural Transition By Humidity Control, PDB code: 7dpj:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7dpj

Go back to Calcium Binding Sites List in 7dpj
Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca203

b:37.0
occ:0.50
 O A:HOH314 2.2 36.1 1.0
OD1 A:ASP30 2.3 40.5 1.0
O A:HOH330 2.4 32.2 0.5
OE2 A:GLU31 2.7 52.0 1.0
CG A:ASP30 3.5 42.1 1.0
CD A:GLU31 3.7 51.0 1.0
OD2 A:ASP30 4.0 47.1 1.0
N A:ASP30 4.3 34.2 1.0
OE1 A:GLU31 4.4 55.0 1.0
CG A:GLU31 4.5 46.8 1.0
NE2 A:HIS27 4.6 26.6 1.0
CB A:ASP30 4.7 39.7 1.0
N A:GLU31 4.8 38.5 1.0
CA A:ASP30 4.9 37.9 1.0
CE1 A:HIS27 4.9 28.0 1.0
O A:PHE28 4.9 25.4 1.0
CB A:GLU31 5.0 43.0 1.0

Calcium binding site 2 out of 3 in 7dpj

Go back to Calcium Binding Sites List in 7dpj
Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca204

b:33.9
occ:1.00
 O A:THR35 2.3 33.6 1.0
OG1 A:THR35 2.5 34.4 1.0
OD1 A:ASP33 2.7 34.1 1.0
OD2 A:ASP33 2.8 35.3 1.0
O A:HOH332 2.9 36.5 1.0
CG A:ASP33 3.1 36.3 1.0
C A:THR35 3.4 33.1 1.0
CB A:THR35 3.6 35.0 1.0
CA A:THR35 3.9 34.6 1.0
N A:THR35 4.2 36.7 1.0
N A:ILE36 4.5 30.2 1.0
CB A:ASP33 4.6 36.7 1.0
CG2 A:THR35 4.9 35.2 1.0
CA A:ILE36 5.0 29.1 1.0

Calcium binding site 3 out of 3 in 7dpj

Go back to Calcium Binding Sites List in 7dpj
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca205

b:29.4
occ:0.46
 OD1 A:ASP105 2.1 30.8 1.0
O A:HOH353 2.3 27.1 0.5
O A:ARG102 2.3 26.5 1.0
OD2 A:ASP105 2.6 31.7 1.0
CG A:ASP105 2.6 30.1 1.0
C A:ARG102 3.4 27.3 1.0
CB A:ASP105 4.1 30.8 1.0
N A:VAL103 4.3 27.4 1.0
CA A:ARG102 4.3 26.4 0.5
CA A:ARG102 4.3 26.9 0.5
CA A:VAL103 4.4 27.3 1.0
O A:VAL103 4.5 25.3 1.0
C A:VAL103 4.6 27.8 1.0
CA A:ASP105 4.6 29.3 1.0
N A:ASP105 4.6 28.1 1.0
CG A:ARG102 4.7 29.1 0.5
CB A:ARG102 4.9 26.8 0.5
CB A:ARG102 5.0 27.9 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: Fri Jul 19 00:08:40 2024

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