Calcium 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:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of E. Coli Glpx with Its Substrate Fructose 1,6-Bisphosphate, PDB code: 3d1r:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca3500 b:21.8 occ:1.00 OE2 A:GLU213 2.0 28.6 1.0 O A:HOH3593 2.3 25.6 1.0 O A:HOH3722 2.4 23.8 1.0 OE1 A:GLU88 2.4 21.8 1.0 OD2 A:ASP85 2.4 22.0 1.0 OD1 A:ASP85 2.5 22.6 1.0 O A:HOH3828 2.5 21.4 1.0 CD A:GLU213 2.6 24.1 1.0 OE1 A:GLU213 2.8 28.2 1.0 CG A:ASP85 2.8 22.0 1.0 CD A:GLU88 3.5 21.3 1.0 CG A:GLU213 3.6 17.8 1.0 O A:HOH3731 4.1 38.1 1.0 CG A:GLU88 4.2 19.1 1.0 O A:HOH3554 4.3 27.7 1.0 O A:HOH3829 4.3 31.4 1.0 O A:HOH3676 4.3 40.4 1.0 C1 A:FBP3499 4.4 20.4 1.0 O A:HOH3544 4.4 24.6 1.0 CB A:ASP85 4.4 18.2 1.0 OE2 A:GLU88 4.5 21.0 1.0 O A:ILE87 4.5 17.0 1.0 O A:HOH3610 4.6 36.2 1.0 O A:HOH3703 4.6 45.2 1.0 C3 A:FBP3499 4.6 22.4 1.0 O2P A:FBP3499 4.7 18.0 1.0 O1P A:FBP3499 4.7 24.7 1.0 CA A:GLU88 4.8 17.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca337 b:28.6 occ:1.00 O A:HOH3538 2.3 36.0 1.0 O A:HOH3544 2.4 24.6 1.0 OD1 A:ASP33 2.4 32.0 1.0 O A:HOH3731 2.4 38.1 1.0 OE1 A:GLU57 2.5 23.8 1.0 OE2 A:GLU57 2.5 29.7 1.0 O A:HOH3829 2.5 31.4 1.0 CD A:GLU57 2.9 24.9 1.0 CG A:ASP33 3.3 27.8 1.0 OD2 A:ASP33 3.4 30.2 1.0 O A:HOH3513 4.1 32.1 1.0 O A:HOH3747 4.2 44.0 1.0 O A:HOH3593 4.2 25.6 1.0 O A:HOH3576 4.3 40.3 1.0 O A:HOH3610 4.3 36.2 1.0 CG A:GLU57 4.4 21.5 1.0 CB A:ASP33 4.7 22.7 1.0 O A:HOH3828 4.7 21.4 1.0 O A:HOH3741 4.8 47.6 1.0 CD A:PRO86 4.8 19.2 1.0 OD1 A:ASP85 4.8 22.6 1.0 O A:ILE87 4.9 17.0 1.0 O A:HOH3774 5.0 40.2 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