Magnesium in PDB 3d1r: Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate

All present enzymatic activity of Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate:
3.1.3.11;

The structure of Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate, PDB code: 3d1r was solved by A.Singer, T.Skarina, A.Dong, G.Brown, A.Joachimiak, A.M.Edwards, A.F.Yakunin, A.Savchenko, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.65 / 1.85
Space group	P 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.296, 91.296, 84.913, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.6

The structure of Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate (pdb code 3d1r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate, PDB code: 3d1r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3502 b:33.0 occ:1.00 O5P A:FBP3499 2.2 31.0 1.0 O A:HOH3762 2.2 34.1 1.0 O A:HOH3763 2.2 34.5 1.0 O A:HOH3761 2.2 32.4 1.0 O A:HOH3759 2.2 33.0 1.0 O A:HOH3675 2.2 33.3 1.0 P2 A:FBP3499 3.3 29.5 1.0 O6P A:FBP3499 3.6 27.6 1.0 O6 A:FBP3499 4.0 28.6 1.0 O A:HOH3768 4.0 57.8 1.0 NZ A:LYS164 4.1 25.2 1.0 O A:HOH3641 4.2 38.6 1.0 O1P A:FBP3499 4.2 24.7 1.0 O A:HOH3561 4.3 26.7 1.0 O5 A:FBP3499 4.4 22.3 1.0 OD1 A:ASP186 4.4 25.6 1.0 O4P A:FBP3499 4.5 25.3 1.0 O1 A:FBP3499 4.7 23.5 1.0 O3P A:FBP3499 4.7 22.1 1.0 P1 A:FBP3499 4.7 26.6 1.0 C6 A:FBP3499 4.9 26.8 1.0

Magnesium binding site 2 out of 2 in the Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3504 b:25.2 occ:1.00 O A:HOH3730 2.2 28.9 1.0 O A:VAL202 2.2 20.8 1.0 O A:SER200 2.2 24.0 1.0 O A:LEU194 2.3 21.4 1.0 O A:MET197 2.6 28.1 1.0 C A:SER200 3.2 23.4 1.0 C A:VAL202 3.4 19.0 1.0 CB A:SER200 3.4 26.1 1.0 C A:LEU194 3.4 19.9 1.0 C A:MET197 3.6 29.6 1.0 CA A:SER200 3.8 24.9 1.0 N A:VAL202 3.8 18.5 1.0 OG A:SER200 3.9 24.9 1.0 CA A:VAL202 4.0 18.4 1.0 O A:HOH3751 4.0 51.0 1.0 N A:SER200 4.0 27.2 1.0 N A:MET197 4.1 27.1 1.0 O A:HOH3524 4.1 35.2 1.0 C A:THR195 4.2 21.6 1.0 CA A:THR195 4.2 20.1 1.0 C A:GLU201 4.2 20.4 1.0 N A:THR195 4.2 20.1 1.0 O A:THR195 4.3 22.4 1.0 N A:GLU201 4.3 21.8 1.0 CA A:MET197 4.4 28.8 1.0 CB A:VAL202 4.4 17.4 1.0 N A:ASP203 4.5 19.5 1.0 CA A:LEU194 4.5 19.0 1.0 N A:PRO198 4.6 31.1 1.0 O A:HOH3622 4.6 25.8 1.0 CB A:MET197 4.7 29.1 1.0 CA A:GLU201 4.7 20.7 1.0 N A:CYS196 4.7 22.2 1.0 CA A:PRO198 4.7 31.4 1.0 C A:PRO198 4.8 32.1 1.0 O A:PRO198 4.8 32.0 1.0 O A:GLU201 4.8 19.1 1.0 CB A:LEU194 4.8 19.1 1.0 CA A:ASP203 5.0 19.0 1.0

G.Brown, A.Singer, V.V.Lunin, M.Proudfoot, T.Skarina, R.Flick, S.Kochinyan, R.Sanishvili, A.Joachimiak, A.M.Edwards, A.Savchenko, A.F.Yakunin. Structural and Biochemical Characterization of the Type II Fructose-1,6-Bisphosphatase Glpx From Escherichia Coli. J.Biol.Chem. V. 284 3784 2009.
ISSN: ISSN 0021-9258
PubMed: 19073594
DOI: 10.1074/JBC.M808186200