Magnesium in PDB 4dls: H-Ras Set 1 CACL2 'Mixed'

The structure of H-Ras Set 1 CACL2 'Mixed', PDB code: 4dls 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)	25.70 / 1.82
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.029, 89.029, 135.207, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 19.4

The structure of H-Ras Set 1 CACL2 'Mixed' also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the H-Ras Set 1 CACL2 'Mixed' (pdb code 4dls). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the H-Ras Set 1 CACL2 'Mixed', PDB code: 4dls:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the H-Ras Set 1 CACL2 'Mixed'


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 1 CACL2 'Mixed' within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:26.6 occ:1.00 O2G A:GNP205 2.1 26.8 1.0 O2B A:GNP205 2.1 22.5 1.0 O A:HOH311 2.1 24.8 1.0 OG A:SER17 2.1 22.2 0.6 OG1 A:THR35 2.2 23.8 0.6 OG1 A:THR35 2.2 24.3 0.4 O A:HOH310 2.3 25.6 1.0 OG A:SER17 2.3 21.9 0.4 CB A:THR35 3.0 23.3 0.6 PG A:GNP205 3.2 24.6 1.0 PB A:GNP205 3.2 24.1 1.0 CB A:SER17 3.2 23.7 0.4 CB A:THR35 3.2 22.9 0.4 CB A:SER17 3.2 20.0 0.6 N3B A:GNP205 3.3 23.6 1.0 N A:THR35 3.8 23.1 0.4 N A:THR35 3.8 26.2 0.6 N A:SER17 3.9 20.5 0.6 OD2 A:ASP57 3.9 26.1 0.6 N A:SER17 3.9 20.2 0.4 O3G A:GNP205 4.0 27.9 1.0 CA A:THR35 4.1 26.2 0.6 CG2 A:THR35 4.1 23.5 0.6 CA A:SER17 4.1 22.0 0.6 OD1 A:ASP57 4.1 24.2 0.6 O2A A:GNP205 4.1 23.5 1.0 CA A:SER17 4.1 21.2 0.4 CA A:THR35 4.2 26.8 0.4 OD2 A:ASP57 4.2 25.8 0.4 O A:HOH324 4.2 29.9 1.0 O1B A:GNP205 4.2 23.5 1.0 O3A A:GNP205 4.2 22.6 1.0 OD1 A:ASP57 4.3 24.2 0.4 O A:THR58 4.3 22.3 0.6 CG2 A:THR35 4.3 28.5 0.4 O1G A:GNP205 4.3 26.3 1.0 O A:ASP33 4.4 24.9 0.4 CG A:ASP57 4.4 26.4 0.6 PA A:GNP205 4.5 22.5 1.0 O A:ASP33 4.5 24.9 0.6 O A:THR58 4.6 30.6 0.4 CG A:ASP57 4.6 25.9 0.4 O1A A:GNP205 4.7 21.1 1.0 C A:PRO34 4.7 27.0 0.6 CB A:LYS16 4.8 21.9 0.6 C A:PRO34 4.8 29.3 0.4 CB A:LYS16 4.9 22.0 0.4 C A:LYS16 4.9 22.6 0.6 NZ A:LYS16 5.0 22.7 0.4 CA A:PRO34 5.0 25.4 0.6

Magnesium binding site 2 out of 2 in the H-Ras Set 1 CACL2 'Mixed'


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 1 CACL2 'Mixed' within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:40.5 occ:0.50 O A:HOH318 2.4 40.1 1.0 O A:HOH314 2.5 34.2 1.0 O A:HOH397 3.0 44.4 0.3 NE2 A:GLN129 3.7 48.7 0.5 NE2 A:GLN129 4.0 33.6 0.5 O A:THR124 4.1 26.9 0.5 O A:HOH327 4.4 34.8 1.0 O A:THR124 4.5 26.3 0.5 CD A:GLN129 4.6 34.1 0.5 OE1 A:GLN129 4.6 17.8 0.5 CD A:GLN129 4.9 31.0 0.5

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