Magnesium in PDB 4dlz: H-Ras Set 2 Ca(Oac)2/Dte, Ordered Off

The structure of H-Ras Set 2 Ca(Oac)2/Dte, Ordered Off, PDB code: 4dlz 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)	26.54 / 1.66
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.261, 88.261, 134.403, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.4

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

Calcium

(Ca)

2 atoms

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

Magnesium binding site 1 out of 3 in the H-Ras Set 2 Ca(Oac)2/Dte, 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 Set 2 Ca(Oac)2/Dte, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:14.4 occ:1.00 O2G A:GNP208 2.1 13.7 1.0 OG A:SER17 2.1 11.0 1.0 O A:HOH431 2.1 13.5 1.0 O2B A:GNP208 2.1 11.6 1.0 OG1 A:THR35 2.1 12.4 1.0 O A:HOH301 2.2 12.7 1.0 CB A:THR35 3.1 12.9 1.0 CB A:SER17 3.1 11.7 1.0 PG A:GNP208 3.2 13.8 1.0 PB A:GNP208 3.3 13.8 1.0 N3B A:GNP208 3.4 13.0 1.0 N A:SER17 3.8 12.1 1.0 N A:THR35 3.8 12.8 1.0 OD2 A:ASP57 3.9 17.3 1.0 CA A:SER17 4.0 11.2 1.0 O3G A:GNP208 4.1 16.3 1.0 CA A:THR35 4.1 15.1 1.0 O A:HOH341 4.1 20.7 1.0 OD1 A:ASP57 4.1 16.1 1.0 CG2 A:THR35 4.2 14.7 1.0 O2A A:GNP208 4.2 14.9 1.0 O3A A:GNP208 4.3 10.6 1.0 O1B A:GNP208 4.3 12.5 1.0 O1G A:GNP208 4.4 14.6 1.0 CG A:ASP57 4.4 16.1 1.0 O A:ASP33 4.5 14.8 1.0 PA A:GNP208 4.5 12.4 1.0 O A:THR58 4.5 15.7 1.0 O1A A:GNP208 4.6 11.5 1.0 C A:PRO34 4.8 18.3 1.0 CB A:LYS16 4.8 10.5 1.0 C A:LYS16 4.9 12.9 1.0 CE A:LYS16 5.0 14.2 1.0

Magnesium binding site 2 out of 3 in the H-Ras Set 2 Ca(Oac)2/Dte, 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 Set 2 Ca(Oac)2/Dte, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:24.9 occ:0.33 O A:HOH355 2.2 26.1 1.0 O A:HOH336 2.3 21.2 1.0 O A:HOH408 3.0 42.7 0.3 NE2 A:GLN129 4.0 20.5 0.6 OE1 A:GLN129 4.1 18.6 0.5 O A:THR124 4.2 14.9 1.0 O A:HOH333 4.4 23.1 1.0 OE1 A:GLN129 4.5 20.3 0.6 CD A:GLN129 4.7 21.6 0.6 CD A:GLN129 4.8 21.5 0.5 NE2 A:GLN129 4.9 16.7 0.5

Magnesium binding site 3 out of 3 in the H-Ras Set 2 Ca(Oac)2/Dte, 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 Set 2 Ca(Oac)2/Dte, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:29.9 occ:1.00 O A:GLU3 2.4 22.5 1.0 O A:HOH436 2.5 43.2 1.0 OE2 A:GLU76 2.5 34.2 1.0 O A:HOH455 2.6 41.1 1.0 OE1 A:GLU76 2.7 21.2 1.0 CD A:GLU76 3.0 30.8 1.0 O A:HOH407 3.0 46.3 1.0 C A:GLU3 3.5 22.9 1.0 CA A:GLU3 4.4 21.4 1.0 CB A:GLU3 4.4 25.1 1.0 N A:GLU3 4.4 20.9 1.0 N A:TYR4 4.5 16.9 1.0 CG A:GLU76 4.5 18.1 1.0 CA A:TYR4 4.6 16.1 1.0 OE2 A:GLU3 4.8 49.2 1.0 N A:LYS5 4.8 15.2 1.0 CG A:GLU3 5.0 25.2 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