Calcium in PDB 4dlr: H-Ras Peg 400/Ca(Oac)2, Ordered Off

The structure of H-Ras Peg 400/Ca(Oac)2, Ordered Off, PDB code: 4dlr 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)	32.92 / 1.32
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	87.415, 87.415, 133.471, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 18.6

The structure of H-Ras Peg 400/Ca(Oac)2, Ordered Off also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the H-Ras Peg 400/Ca(Oac)2, Ordered Off (pdb code 4dlr). 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 Peg 400/Ca(Oac)2, Ordered Off, PDB code: 4dlr:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the H-Ras Peg 400/Ca(Oac)2, Ordered Off


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of H-Ras Peg 400/Ca(Oac)2, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:10.1 occ:1.00 O A:PHE28 2.3 10.2 1.0 OD1 A:ASP30 2.4 12.2 1.0 O A:HOH307 2.5 16.9 1.0 O A:HOH442 2.5 18.2 1.0 C A:PHE28 3.6 9.4 1.0 CG A:ASP30 3.6 12.4 1.0 N A:ASP30 4.0 9.5 1.0 O A:HOH367 4.3 26.0 1.0 CA A:VAL29 4.3 8.8 1.0 CB A:ASP30 4.4 11.6 1.0 O A:HOH310 4.4 17.8 1.0 O A:HOH412 4.4 36.4 1.0 N A:VAL29 4.4 8.4 1.0 OD2 A:ASP30 4.5 14.4 1.0 CA A:PHE28 4.6 9.1 1.0 O A:HOH404 4.6 28.2 1.0 C A:VAL29 4.6 9.9 1.0 N A:PHE28 4.7 9.5 1.0 CB A:PHE28 4.8 10.6 1.0 CA A:ASP30 4.8 10.7 1.0 CD2 A:PHE28 4.9 11.4 1.0

Calcium binding site 2 out of 3 in the H-Ras Peg 400/Ca(Oac)2, Ordered Off


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of H-Ras Peg 400/Ca(Oac)2, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:24.9 occ:1.00 O A:GLU3 2.4 17.5 1.0 OE2 A:GLU76 2.5 21.9 1.0 O A:HOH423 2.7 31.1 1.0 OE1 A:GLU76 2.7 15.4 1.0 O A:HOH460 2.8 38.8 1.0 O A:HOH455 2.8 38.6 1.0 CD A:GLU76 3.0 17.6 1.0 O A:HOH408 3.2 30.5 1.0 C A:GLU3 3.5 14.5 1.0 CB A:GLU3 4.2 19.2 1.0 CA A:GLU3 4.3 15.6 1.0 N A:TYR4 4.4 11.2 1.0 N A:GLU3 4.4 15.9 1.0 CG A:GLU76 4.4 12.3 1.0 CA A:TYR4 4.5 10.3 1.0 CD A:GLU3 4.6 34.8 1.0 OE1 A:GLU3 4.6 41.1 1.0 CG A:GLU3 4.6 23.1 1.0 CG A:LYS5 4.7 19.1 1.0 N A:LYS5 4.7 10.1 1.0

Calcium binding site 3 out of 3 in the H-Ras Peg 400/Ca(Oac)2, Ordered Off


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of H-Ras Peg 400/Ca(Oac)2, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:17.7 occ:0.50 O A:ARG102 2.3 18.2 1.0 OD1 A:ASP105 2.5 28.8 1.0 O A:HOH380 2.7 22.4 0.5 CG A:ASP105 3.1 24.7 1.0 OD2 A:ASP105 3.1 29.3 1.0 C A:ARG102 3.3 17.2 1.0 CA A:VAL103 4.1 16.8 1.0 N A:VAL103 4.2 14.1 1.0 CA A:ARG102 4.2 15.0 1.0 O A:HOH458 4.3 34.2 1.0 C A:VAL103 4.4 18.5 1.0 CB A:ASP105 4.4 21.6 1.0 N A:ASP105 4.5 17.1 1.0 O A:VAL103 4.5 18.4 1.0 O A:HOH403 4.5 30.0 1.0 CA A:ASP105 4.6 18.2 1.0 CB A:ARG102 4.7 17.4 1.0 NH1 A:ARG73 4.9 29.8 1.0

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