Magnesium in PDB 4dly: Set 1 CACL2/Dtt, Ordered Off

The structure of Set 1 CACL2/Dtt, Ordered Off, PDB code: 4dly 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)	28.23 / 1.57
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.207, 88.207, 134.142, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 17.9

The structure of Set 1 CACL2/Dtt, Ordered Off also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Set 1 CACL2/Dtt, Ordered Off (pdb code 4dly). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Set 1 CACL2/Dtt, Ordered Off, PDB code: 4dly:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Set 1 CACL2/Dtt, Ordered Off


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Set 1 CACL2/Dtt, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:10.1 occ:1.00 O2G A:GNP208 2.1 10.3 1.0 O2B A:GNP208 2.1 9.6 1.0 OG A:SER17 2.1 8.5 1.0 O A:HOH437 2.1 9.6 1.0 OG1 A:THR35 2.1 9.8 1.0 O A:HOH301 2.2 10.3 1.0 CB A:THR35 3.1 10.2 1.0 CB A:SER17 3.2 9.8 1.0 PG A:GNP208 3.2 9.7 1.0 PB A:GNP208 3.2 9.5 1.0 N3B A:GNP208 3.3 9.0 1.0 N A:THR35 3.8 10.2 1.0 N A:SER17 3.9 8.6 1.0 OD2 A:ASP57 4.1 11.5 1.0 CA A:THR35 4.1 11.0 1.0 O3G A:GNP208 4.1 11.4 1.0 CA A:SER17 4.1 8.2 1.0 O A:HOH342 4.1 13.4 1.0 O2A A:GNP208 4.1 10.2 1.0 OD1 A:ASP57 4.2 10.6 1.0 CG2 A:THR35 4.2 11.3 1.0 O3A A:GNP208 4.2 8.6 1.0 O1B A:GNP208 4.3 9.6 1.0 O1G A:GNP208 4.3 12.0 1.0 O A:ASP33 4.4 11.2 1.0 CG A:ASP57 4.5 9.1 1.0 PA A:GNP208 4.5 9.2 1.0 O A:THR58 4.6 10.9 1.0 O1A A:GNP208 4.7 9.0 1.0 C A:PRO34 4.8 11.1 1.0 CB A:LYS16 4.8 8.7 1.0 C A:LYS16 4.9 8.2 1.0 CE A:LYS16 5.0 10.2 1.0

Magnesium binding site 2 out of 2 in the Set 1 CACL2/Dtt, Ordered Off


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Set 1 CACL2/Dtt, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:23.6 occ:0.33 O A:HOH357 2.3 24.1 1.0 O A:HOH336 2.4 21.2 1.0 NE2 A:GLN129 4.0 19.8 0.6 O A:THR124 4.1 14.4 1.0 OE1 A:GLN129 4.1 18.0 0.5 OE1 A:GLN129 4.4 19.4 0.6 O A:HOH333 4.4 22.8 1.0 CD A:GLN129 4.6 20.6 0.6 CD A:GLN129 4.7 20.7 0.5 NE2 A:GLN129 4.7 16.4 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