Calcium in PDB 4l9s: Crystal Structure of H-Ras G12C, Gdp-Bound

All present enzymatic activity of Crystal Structure of H-Ras G12C, Gdp-Bound:
3.6.5.2;

The structure of Crystal Structure of H-Ras G12C, Gdp-Bound, PDB code: 4l9s was solved by J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.50 / 1.61
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	92.725, 92.725, 121.897, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 17.3

The structure of Crystal Structure of H-Ras G12C, Gdp-Bound also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of H-Ras G12C, Gdp-Bound (pdb code 4l9s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of H-Ras G12C, Gdp-Bound, PDB code: 4l9s:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of H-Ras G12C, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of H-Ras G12C, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:36.8 occ:0.50 OD1 A:ASP105 2.2 35.4 0.5 O A:ARG102 2.3 28.2 1.0 O A:HOH461 2.3 38.2 0.5 OD2 A:ASP105 2.5 31.0 0.5 CG A:ASP105 2.6 35.0 0.5 HB2 A:ASP105 3.3 44.4 0.5 C A:ARG102 3.5 27.0 1.0 HG2 A:ARG102 3.8 61.9 1.0 HA A:VAL103 3.9 39.8 1.0 HG3 A:ARG102 4.0 61.9 1.0 CB A:ASP105 4.0 36.7 0.5 H A:ASP105 4.0 42.1 1.0 HA A:ARG102 4.1 31.5 1.0 CA A:CA204 4.1 41.5 0.5 CB A:ASP105 4.1 37.0 0.5 OD1 A:ASP105 4.1 40.3 0.5 HA A:ASP105 4.2 40.4 0.5 CG A:ARG102 4.3 51.6 1.0 CA A:ARG102 4.3 26.3 1.0 CG A:ASP105 4.4 39.8 0.5 N A:VAL103 4.4 30.2 1.0 O A:VAL103 4.4 33.6 1.0 CA A:VAL103 4.5 33.2 1.0 CA A:ASP105 4.5 33.7 0.5 N A:ASP105 4.5 35.1 1.0 HB3 A:ASP105 4.5 44.1 0.5 CA A:ASP105 4.5 33.4 0.5 HB2 A:ASP105 4.5 44.1 0.5 C A:VAL103 4.6 31.6 1.0 HB3 A:ASP105 4.9 44.4 0.5 CB A:ARG102 4.9 36.7 1.0 HH11 A:ARG102 4.9 94.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of H-Ras G12C, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of H-Ras G12C, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:41.5 occ:0.50 O A:VAL103 2.3 33.6 1.0 O A:HOH465 2.3 50.3 1.0 OD2 A:ASP105 2.4 31.0 0.5 HB2 A:ASP105 3.4 44.4 0.5 C A:VAL103 3.5 31.6 1.0 CG A:ASP105 3.6 35.0 0.5 HB2 A:ASP105 3.9 44.1 0.5 HA A:LYS104 4.0 37.2 1.0 HA A:VAL103 4.0 39.8 1.0 CA A:CA203 4.1 36.8 0.5 CB A:ASP105 4.3 37.0 0.5 C A:LYS104 4.3 35.4 1.0 CB A:ASP105 4.3 36.7 0.5 HB3 A:ASP105 4.3 44.4 0.5 CA A:VAL103 4.3 33.2 1.0 N A:ASP105 4.4 35.1 1.0 N A:LYS104 4.4 30.4 1.0 H A:ASP105 4.4 42.1 1.0 CA A:LYS104 4.4 31.0 1.0 HG3 A:ARG73 4.4 89.2 1.0 HG12 A:VAL103 4.5 53.9 1.0 HG13 A:VAL103 4.5 53.9 1.0 O A:ARG102 4.5 28.2 1.0 OD1 A:ASP105 4.6 35.4 0.5 O A:LYS104 4.7 39.6 1.0 CG1 A:VAL103 4.9 44.9 1.0 CA A:ASP105 5.0 33.7 0.5 CA A:ASP105 5.0 33.4 0.5

J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat. K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity and Effector Interactions. Nature V. 503 548 2013.
ISSN: ISSN 0028-0836
PubMed: 24256730
DOI: 10.1038/NATURE12796