Calcium in PDB 4dls: H-Ras Set 1 CACL2 'Mixed'

The structure of H-Ras Set 1 CACL2 'Mixed', PDB code: 4dls was solved by G.Holzapfel, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.70 / 1.82
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.029, 89.029, 135.207, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 19.4

The structure of H-Ras Set 1 CACL2 'Mixed' also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the H-Ras Set 1 CACL2 'Mixed' (pdb code 4dls). 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 Set 1 CACL2 'Mixed', PDB code: 4dls:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the H-Ras Set 1 CACL2 'Mixed'


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of H-Ras Set 1 CACL2 'Mixed' within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:29.8 occ:1.00 O A:PHE28 2.4 26.6 0.4 O A:PHE28 2.4 19.6 0.6 O A:HOH326 2.4 31.6 1.0 OD1 A:ASP30 2.5 25.4 0.6 O A:HOH352 2.5 36.1 1.0 OD2 A:ASP30 2.6 27.6 0.4 C A:PHE28 3.5 25.6 0.4 C A:PHE28 3.6 23.7 0.6 CG A:ASP30 3.6 36.8 0.6 CG A:ASP30 3.8 35.9 0.4 N A:ASP30 3.9 25.7 0.6 N A:ASP30 4.1 27.1 0.4 CB A:ASP30 4.3 28.4 0.6 N A:VAL29 4.3 26.5 0.4 CA A:VAL29 4.3 27.2 0.4 CA A:VAL29 4.3 27.2 0.6 O A:HOH375 4.4 50.4 1.0 N A:VAL29 4.4 26.3 0.6 O A:HOH356 4.5 35.7 1.0 N A:PHE28 4.5 24.2 0.4 CA A:PHE28 4.5 22.9 0.4 OD1 A:ASP30 4.5 27.6 0.4 CA A:PHE28 4.6 23.4 0.6 OD2 A:ASP30 4.6 31.4 0.6 C A:VAL29 4.6 28.2 0.6 C A:VAL29 4.7 28.1 0.4 CB A:ASP30 4.7 31.4 0.4 N A:PHE28 4.7 22.1 0.6 CA A:ASP30 4.7 27.3 0.6 CB A:PHE28 4.7 24.0 0.6 ND1 A:HIS27 4.9 29.0 0.4 CB A:PHE28 4.9 24.4 0.4 CD2 A:PHE28 5.0 27.2 0.6

Calcium binding site 2 out of 2 in the H-Ras Set 1 CACL2 'Mixed'


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of H-Ras Set 1 CACL2 'Mixed' within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:57.3 occ:0.50 O A:ARG102 2.5 28.3 0.5 OD2 A:ASP105 2.5 42.8 0.5 O A:HOH409 2.7 56.7 0.5 OD1 A:ASP105 3.0 39.8 0.5 CG A:ASP105 3.0 27.6 0.5 O A:VAL103 3.4 42.9 0.5 C A:ARG102 3.5 36.1 0.5 CA A:VAL103 3.6 39.1 0.5 O A:ARG102 3.8 38.0 0.5 C A:VAL103 3.9 40.8 0.5 CG A:ARG102 4.2 36.5 0.5 CA A:ARG102 4.4 26.8 0.5 N A:VAL103 4.4 31.4 0.5 CB A:ASP105 4.4 34.0 0.5 C A:ARG102 4.4 40.6 0.5 N A:VAL103 4.4 31.2 0.5 CA A:VAL103 4.4 31.6 0.5 CB A:VAL103 4.5 24.8 0.5 NH1 A:ARG73 4.6 54.0 0.5 N A:ASP105 4.6 29.5 0.5 CA A:ASP105 4.7 36.6 0.5 C A:VAL103 4.7 39.8 0.5 CG2 A:VAL103 4.7 30.2 0.5 CG1 A:VAL103 4.8 33.2 0.5 CB A:ARG102 4.9 38.5 0.5 O A:VAL103 4.9 37.6 0.5

G.Holzapfel, G.Buhrman, C.Mattos. Shift in the Equilibrium Between on and Off States of the Allosteric Switch in Ras-Gppnhp Affected By Small Molecules and Bulk Solvent Composition. Biochemistry V. 51 6114 2012.
ISSN: ISSN 0006-2960
PubMed: 22845804
DOI: 10.1021/BI300509J