Magnesium in PDB 3v4f: H-Ras Peg 400/CACL2, Ordered Off

The structure of H-Ras Peg 400/CACL2, Ordered Off, PDB code: 3v4f 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)	33.27 / 1.39
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.521, 88.521, 134.060, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 19.8

The structure of H-Ras Peg 400/CACL2, Ordered Off also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the H-Ras Peg 400/CACL2, Ordered Off (pdb code 3v4f). 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 Peg 400/CACL2, Ordered Off, PDB code: 3v4f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the H-Ras Peg 400/CACL2, 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/CACL2, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg192 b:11.7 occ:1.00 O2G A:GNP190 2.0 14.0 1.0 O2B A:GNP190 2.1 12.0 1.0 OG A:SER17 2.1 11.6 1.0 O A:HOH544 2.1 13.4 1.0 OG1 A:THR35 2.1 13.5 1.0 O A:HOH301 2.1 14.0 1.0 CB A:THR35 3.1 12.9 1.0 CB A:SER17 3.2 12.5 1.0 PG A:GNP190 3.2 12.7 1.0 PB A:GNP190 3.2 11.2 1.0 N3B A:GNP190 3.4 12.3 1.0 N A:THR35 3.8 14.3 1.0 N A:SER17 3.9 10.4 1.0 O3G A:GNP190 4.0 16.1 1.0 OD2 A:ASP57 4.1 17.6 1.0 CA A:THR35 4.1 13.3 1.0 CA A:SER17 4.1 10.2 1.0 O2A A:GNP190 4.1 12.8 1.0 OD1 A:ASP57 4.1 17.9 1.0 O A:HOH348 4.2 19.5 1.0 CG2 A:THR35 4.2 15.3 1.0 O3A A:GNP190 4.2 10.5 1.0 O1B A:GNP190 4.3 10.6 1.0 O1G A:GNP190 4.4 13.9 1.0 O A:ASP33 4.4 14.2 1.0 CG A:ASP57 4.5 15.4 1.0 PA A:GNP190 4.5 11.1 1.0 O A:THR58 4.6 14.5 1.0 O1A A:GNP190 4.7 10.8 1.0 C A:PRO34 4.8 14.8 1.0 CB A:LYS16 4.9 9.4 1.0 C A:LYS16 5.0 8.9 1.0 CE A:LYS16 5.0 13.0 1.0

Magnesium binding site 2 out of 2 in the H-Ras Peg 400/CACL2, 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/CACL2, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg194 b:29.0 occ:0.33 O A:HOH364 2.4 32.3 1.0 O A:HOH342 2.6 29.1 1.0 O A:HOH440 2.9 39.6 0.3 NE2 A:GLN129 4.1 27.9 0.5 O A:THR124 4.1 18.4 1.0 OE1 A:GLN129 4.3 19.4 0.5 O A:HOH338 4.4 29.7 1.0 NE2 A:GLN129 4.4 26.7 0.5 CD A:GLN129 4.6 23.7 0.5 OE1 A:GLN129 4.8 21.2 0.5 CD A:GLN129 5.0 26.1 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