Calcium in PDB 7jii: Hras A59E Gdp

The structure of Hras A59E Gdp, PDB code: 7jii was solved by C.W.Johnson, K.M.Haigis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.14 / 1.53
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.593, 37.946, 56.254, 107.36, 107.19, 95.32
R / Rfree (%)	15.8 / 20.3

The structure of Hras A59E Gdp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Hras A59E Gdp (pdb code 7jii). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Hras A59E Gdp, PDB code: 7jii:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Hras A59E Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hras A59E Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:21.2 occ:1.00 O A:HOH322 2.3 20.5 1.0 OD1 A:ASP33 2.3 22.2 1.0 O A:HOH317 2.4 19.6 1.0 O A:HOH412 2.5 18.9 1.0 O A:HOH415 2.5 19.2 1.0 CG A:ASP33 3.3 23.8 1.0 OD2 A:ASP33 3.6 24.4 1.0 O A:HOH308 3.7 30.9 1.0 O1A A:GDP201 3.8 15.8 1.0 OE1 A:GLU31 4.4 18.8 1.0 O A:HOH347 4.6 17.5 1.0 CB A:ASP33 4.7 24.4 1.0 OE2 A:GLU31 4.7 17.4 1.0 O A:GLU31 4.7 20.1 1.0 O A:TYR32 4.8 21.5 1.0 CD A:GLU31 4.8 17.5 1.0 C5' A:GDP201 4.9 14.9 1.0

Calcium binding site 2 out of 4 in the Hras A59E Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hras A59E Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:47.4 occ:1.00 O A:GLY138 2.6 18.9 1.0 O A:HOH443 2.6 29.5 1.0 O A:HOH323 2.6 30.3 1.0 O A:HOH452 2.9 26.6 1.0 C A:GLY138 3.7 22.2 1.0 O A:HOH373 4.1 34.9 1.0 CA A:GLY138 4.2 16.5 1.0 O A:HOH431 4.4 29.7 1.0 OE1 A:GLU162 4.6 18.8 1.0 N A:ILE139 4.8 17.7 1.0 O A:HOH346 4.8 17.5 1.0

Calcium binding site 3 out of 4 in the Hras A59E Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hras A59E Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:32.3 occ:1.00 O B:GLU3 2.3 22.0 1.0 OE2 B:GLU76 2.4 26.2 1.0 OE1 B:GLU76 2.7 20.6 1.0 CD B:GLU76 2.9 22.1 1.0 C B:GLU3 3.5 22.8 1.0 N B:GLU3 4.3 23.7 1.0 CA B:GLU3 4.3 25.2 1.0 CG B:GLU76 4.4 19.8 1.0 CB B:GLU3 4.5 22.9 1.0 N B:TYR4 4.5 20.7 1.0 CA B:TYR4 4.6 18.9 1.0 CG2 B:THR2 4.7 23.5 1.0 N B:LYS5 4.9 19.0 1.0

Calcium binding site 4 out of 4 in the Hras A59E Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hras A59E Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:43.5 occ:1.00 O B:HOH431 2.3 26.8 1.0 O B:GLY138 2.5 17.6 1.0 O B:HOH314 2.6 29.3 1.0 O B:HOH454 2.7 38.4 1.0 O B:HOH424 3.0 32.3 1.0 C B:GLY138 3.7 17.0 1.0 OD1 B:ASP108 4.3 32.3 1.0 OE1 B:GLU162 4.3 19.1 1.0 CA B:GLY138 4.3 15.2 1.0 O B:HOH333 4.4 21.0 1.0 N B:ILE139 4.7 15.6 1.0 O B:HOH378 5.0 32.1 1.0 CA B:ILE139 5.0 14.3 1.0 O B:HOH343 5.0 33.0 1.0

C.W.Johnson, H.S.Seo, E.M.Terrell, M.H.Yang, F.Kleinjan, T.Gebregiworgis, G.M.C.Gasmi-Seabrook, E.A.Geffken, J.Lakhani, K.Song, P.Bashyal, O.Popow, J.A.Paulo, A.Liu, C.Mattos, C.B.Marshall, M.Ikura, D.K.Morrison, S.Dhe-Paganon, K.M.Haigis. Regulation of Gtpase Function By Autophosphorylation. Mol.Cell V. 82 950 2022.
ISSN: ISSN 1097-2765
PubMed: 35202574
DOI: 10.1016/J.MOLCEL.2022.02.011