Magnesium in PDB 4dlx: H-Ras Set 1 CACL2/Dte, Ordered Off

The structure of H-Ras Set 1 CACL2/Dte, Ordered Off, PDB code: 4dlx 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)	26.48 / 1.73
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.085, 88.085, 133.900, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.8

The structure of H-Ras Set 1 CACL2/Dte, Ordered Off also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the H-Ras Set 1 CACL2/Dte, Ordered Off (pdb code 4dlx). 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 1 CACL2/Dte, Ordered Off, PDB code: 4dlx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the H-Ras Set 1 CACL2/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 1 CACL2/Dte, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:14.4 occ:1.00 O2G A:GNP206 2.1 13.3 1.0 O2B A:GNP206 2.1 10.8 1.0 OG A:SER17 2.1 10.8 1.0 O A:HOH437 2.1 12.7 1.0 OG1 A:THR35 2.2 14.6 1.0 O A:HOH301 2.2 13.7 1.0 CB A:THR35 3.1 13.2 1.0 CB A:SER17 3.1 14.6 1.0 PG A:GNP206 3.2 14.2 1.0 PB A:GNP206 3.2 13.3 1.0 N3B A:GNP206 3.4 11.1 1.0 N A:THR35 3.8 15.1 1.0 N A:SER17 3.9 10.6 1.0 O3G A:GNP206 4.0 15.6 1.0 OD2 A:ASP57 4.0 16.5 1.0 CA A:SER17 4.1 10.8 1.0 O A:HOH342 4.1 17.4 1.0 CA A:THR35 4.1 13.1 1.0 O2A A:GNP206 4.1 14.5 1.0 OD1 A:ASP57 4.2 13.9 1.0 CG2 A:THR35 4.2 13.7 1.0 O1B A:GNP206 4.3 12.8 1.0 O3A A:GNP206 4.3 11.6 1.0 O1G A:GNP206 4.4 14.1 1.0 O A:ASP33 4.4 14.8 1.0 CG A:ASP57 4.5 14.4 1.0 PA A:GNP206 4.5 13.1 1.0 O A:THR58 4.6 15.3 1.0 O1A A:GNP206 4.6 10.9 1.0 C A:PRO34 4.8 17.9 1.0 CB A:LYS16 4.9 11.3 1.0 C A:LYS16 4.9 12.3 1.0

Magnesium binding site 2 out of 3 in the H-Ras Set 1 CACL2/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 1 CACL2/Dte, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:40.2 occ:0.33 O A:HOH357 2.4 34.5 1.0 O A:HOH336 2.5 27.3 1.0 OE1 A:GLN129 4.1 29.3 1.0 O A:THR124 4.1 17.8 1.0 O A:HOH333 4.2 28.7 1.0 CD A:GLN129 4.7 29.3 1.0 NE2 A:GLN129 4.7 31.2 1.0

Magnesium binding site 3 out of 3 in the H-Ras Set 1 CACL2/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 1 CACL2/Dte, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:18.3 occ:0.50 O A:ARG102 2.3 24.4 1.0 OD2 A:ASP105 2.4 37.0 1.0 OD1 A:ASP105 2.9 39.1 1.0 CG A:ASP105 2.9 32.3 1.0 C A:ARG102 3.4 29.9 1.0 CG A:ARG102 4.1 32.6 0.5 CG A:ARG102 4.2 32.8 0.6 CA A:VAL103 4.2 23.2 1.0 N A:VAL103 4.2 20.4 1.0 CA A:ARG102 4.3 25.7 0.5 CA A:ARG102 4.3 25.7 0.6 O A:HOH452 4.3 37.2 1.0 CB A:ASP105 4.3 28.2 1.0 O A:HOH404 4.3 41.0 1.0 C A:VAL103 4.5 27.0 1.0 N A:ASP105 4.5 25.4 1.0 O A:VAL103 4.6 26.8 1.0 CA A:ASP105 4.7 24.5 1.0 NH1 A:ARG73 4.8 39.7 1.0 CB A:ARG102 4.8 26.4 0.5 CB A:ARG102 4.8 26.4 0.6

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