Calcium in PDB 3k8y: Allosteric Modulation of H-Ras Gtpase

The structure of Allosteric Modulation of H-Ras Gtpase, PDB code: 3k8y was solved by G.Holzapfel, G.Buhrman, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.99 / 1.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.475, 88.475, 134.906, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22.7

The structure of Allosteric Modulation of H-Ras Gtpase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Allosteric Modulation of H-Ras Gtpase (pdb code 3k8y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Allosteric Modulation of H-Ras Gtpase, PDB code: 3k8y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Allosteric Modulation of H-Ras Gtpase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Allosteric Modulation of H-Ras Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca167 b:16.2 occ:1.00 O A:PHE28 2.4 15.2 1.0 OD1 A:ASP30 2.5 20.6 1.0 O A:HOH200 2.5 24.0 1.0 O A:HOH233 2.6 25.0 1.0 C A:PHE28 3.6 15.2 1.0 CG A:ASP30 3.7 20.4 1.0 N A:ASP30 4.1 15.7 1.0 CA A:VAL29 4.3 15.6 1.0 O A:HOH240 4.4 24.5 1.0 N A:VAL29 4.4 14.4 1.0 O A:HOH275 4.4 32.0 1.0 CB A:ASP30 4.5 18.1 1.0 OD2 A:ASP30 4.6 22.8 1.0 CA A:PHE28 4.6 15.7 1.0 C A:VAL29 4.7 15.8 1.0 O A:HOH185 4.7 30.5 1.0 N A:PHE28 4.7 15.5 1.0 CB A:PHE28 4.8 16.1 1.0 CA A:ASP30 4.9 15.7 1.0 ND1 A:HIS27 5.0 17.1 1.0

Calcium binding site 2 out of 2 in the Allosteric Modulation of H-Ras Gtpase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Allosteric Modulation of H-Ras Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca169 b:26.9 occ:1.00 O A:ASP107 2.4 30.2 1.0 O A:TYR137 2.5 22.9 1.0 O A:HOH232 2.6 28.4 1.0 O A:HOH392 2.6 32.0 1.0 OXT A:ACT719 2.6 29.1 1.0 O A:ACT719 2.7 29.4 1.0 O A:HOH366 2.8 35.3 1.0 C A:ACT719 3.1 29.6 1.0 C A:ASP107 3.5 29.7 1.0 C A:TYR137 3.6 19.2 1.0 CA A:ASP108 4.1 26.8 1.0 N A:ASP108 4.2 28.0 1.0 CA A:TYR137 4.3 19.9 1.0 OD1 A:ASP108 4.4 41.7 1.0 NH2 A:ARG97 4.4 28.6 1.0 CE A:MET111 4.5 26.2 1.0 CA A:ASP107 4.5 32.2 1.0 N A:VAL109 4.6 22.6 1.0 O A:HOH299 4.6 36.5 1.0 CB A:TYR137 4.6 20.0 1.0 CH3 A:ACT719 4.6 29.0 1.0 O A:HOH197 4.6 28.3 1.0 N A:GLY138 4.7 17.2 1.0 C A:ASP108 4.7 28.3 1.0 CG2 A:ILE139 4.8 17.8 1.0 O A:VAL109 4.9 18.5 1.0 CA A:GLY138 4.9 20.4 1.0 O A:HOH216 4.9 43.2 1.0

G.Buhrman, G.Holzapfel, S.Fetics, C.Mattos. Allosteric Modulation of Ras Positions Q61 For A Direct Role in Catalysis. Proc.Natl.Acad.Sci.Usa V. 107 4931 2010.
ISSN: ISSN 0027-8424
PubMed: 20194776
DOI: 10.1073/PNAS.0912226107