Magnesium 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:

Calcium

(Ca)

3 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg202 b:8.5 occ:1.00 O2G A:GNP208 2.0 10.5 1.0 O2B A:GNP208 2.1 8.2 1.0 O A:HOH438 2.1 9.2 1.0 OG A:SER17 2.1 8.7 1.0 OG1 A:THR35 2.1 9.2 1.0 O A:HOH301 2.1 10.1 1.0 CB A:THR35 3.1 9.5 1.0 CB A:SER17 3.2 8.2 1.0 PG A:GNP208 3.2 8.8 1.0 PB A:GNP208 3.2 8.0 1.0 N3B A:GNP208 3.3 9.6 1.0 N A:THR35 3.8 10.2 1.0 N A:SER17 3.9 7.5 1.0 O3G A:GNP208 4.0 11.2 1.0 OD2 A:ASP57 4.1 10.8 1.0 CA A:THR35 4.1 10.3 1.0 CA A:SER17 4.1 7.9 1.0 O2A A:GNP208 4.1 8.9 1.0 O A:HOH342 4.1 13.1 1.0 OD1 A:ASP57 4.2 10.6 1.0 CG2 A:THR35 4.2 11.6 1.0 O3A A:GNP208 4.2 8.1 1.0 O1B A:GNP208 4.3 8.8 1.0 O1G A:GNP208 4.4 9.8 1.0 O A:ASP33 4.4 10.6 1.0 CG A:ASP57 4.5 9.7 1.0 PA A:GNP208 4.5 8.1 1.0 O A:THR58 4.5 10.8 1.0 O1A A:GNP208 4.7 8.9 1.0 C A:PRO34 4.8 11.7 1.0 CB A:LYS16 4.8 7.7 1.0 C A:LYS16 4.9 7.4 1.0 CE A:LYS16 5.0 9.4 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg206 b:20.5 occ:0.33 O A:HOH356 2.2 20.6 1.0 O A:HOH337 2.3 20.9 1.0 O A:HOH409 3.5 39.1 0.3 O A:THR124 3.9 14.1 1.0 NE2 A:GLN129 4.1 17.6 0.6 OE1 A:GLN129 4.1 15.9 0.4 O A:HOH334 4.3 21.3 1.0 OE1 A:GLN129 4.4 17.4 0.6 CD A:GLN129 4.7 16.8 0.6 CD A:GLN129 4.7 18.6 0.4 NE2 A:GLN129 4.8 12.9 0.4 C A:THR124 5.0 11.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg207 b:32.4 occ:0.50 OE2 A:GLU162 2.3 16.4 1.0 O A:HOH400 2.4 11.7 1.0 O A:HOH388 2.5 28.4 0.5 CD A:GLU162 3.4 12.1 1.0 O A:HOH448 3.6 20.9 1.0 NE2 A:GLN165 3.8 14.1 1.0 OE1 A:GLU162 3.8 16.1 1.0 O A:HOH341 3.9 21.1 1.0 CD A:PRO140 4.0 10.4 1.0 CG A:PRO140 4.1 12.6 1.0 O A:HOH353 4.2 25.4 1.0 OE1 A:GLN165 4.3 18.4 1.0 CD A:GLN165 4.5 14.4 1.0 CG A:GLU162 4.6 12.6 1.0 CB A:PRO140 4.7 10.9 1.0 N A:PRO140 5.0 8.8 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