Magnesium in PDB 3r1m: Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form)

The structure of Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form), PDB code: 3r1m was solved by S.Fushinobu, H.Nishimasu, D.Hattori, H.-J.Song, T.Wakagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.22 / 1.50
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.543, 112.543, 153.608, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.5

The binding sites of Magnesium atom in the Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form) (pdb code 3r1m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form), PDB code: 3r1m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:17.8 occ:1.00 O A:LYS232 2.0 20.7 1.0 O A:HOH389 2.1 18.9 1.0 O A:HOH388 2.1 19.9 1.0 O1P A:13P401 2.1 18.0 1.0 OD2 A:ASP234 2.2 15.6 1.0 O A:HOH386 2.2 14.2 1.0 P A:13P401 3.1 17.3 1.0 CG A:ASP234 3.1 15.6 1.0 C A:LYS232 3.2 20.5 1.0 MG A:MG403 3.4 12.1 1.0 O2P A:13P401 3.5 12.6 1.0 N A:LYS232 3.5 21.7 1.0 O3P A:13P401 3.7 17.6 1.0 CA A:LYS232 3.8 21.3 1.0 OD1 A:ASP54 3.9 14.3 1.0 OD1 A:ASP234 3.9 15.9 1.0 CB A:ASP234 3.9 15.2 1.0 CB A:LYS232 4.2 21.7 1.0 OD2 A:ASP96 4.2 18.8 1.0 C A:ASP233 4.2 18.8 1.0 N A:ASP233 4.3 20.3 1.0 O A:ASP233 4.3 19.2 1.0 C A:GLY231 4.3 22.9 1.0 CD1 A:LEU222 4.3 35.2 1.0 OD2 A:ASP54 4.3 14.1 1.0 OD2 A:ASP12 4.4 15.2 1.0 OD1 A:ASP96 4.4 21.6 1.0 N A:ASP234 4.5 18.0 1.0 CG A:ASP54 4.5 14.3 1.0 CA A:GLY231 4.6 23.5 1.0 O1 A:13P401 4.6 19.2 1.0 CA A:ASP233 4.6 20.3 1.0 NE2 A:GLN95 4.6 20.5 1.0 CB A:ASP12 4.7 14.6 1.0 CG A:ASP96 4.7 22.2 1.0 CA A:ASP234 4.9 15.6 1.0 OD1 A:ASP53 4.9 12.9 1.0 NZ A:LYS10 4.9 16.4 1.0 OD1 A:ASP132 5.0 13.6 1.0

Magnesium binding site 2 out of 3 in the Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:12.1 occ:1.00 O2P A:13P401 2.0 12.6 1.0 OD1 A:ASP53 2.0 12.9 1.0 OD1 A:ASP132 2.0 13.6 1.0 OD2 A:ASP54 2.0 14.1 1.0 O A:HOH386 2.1 14.2 1.0 OD2 A:ASP234 2.1 15.6 1.0 CG A:ASP234 3.0 15.6 1.0 CG A:ASP54 3.0 14.3 1.0 CG A:ASP132 3.1 11.6 1.0 CG A:ASP53 3.1 13.1 1.0 P A:13P401 3.2 17.3 1.0 MG A:MG402 3.4 17.8 1.0 OD1 A:ASP54 3.4 14.3 1.0 OD2 A:ASP53 3.5 14.2 1.0 O1P A:13P401 3.6 18.0 1.0 OD2 A:ASP132 3.7 13.6 1.0 NZ A:LYS133 3.7 12.2 1.0 OD1 A:ASP234 3.8 15.9 1.0 O3P A:13P401 3.9 17.6 1.0 CB A:ASP234 3.9 15.2 1.0 OD2 A:ASP12 4.0 15.2 1.0 CB A:ASP132 4.2 11.3 1.0 CB A:ASP54 4.3 12.9 1.0 N A:ASP54 4.4 12.5 1.0 N A:LYS133 4.4 10.4 1.0 O1 A:13P401 4.4 19.2 1.0 CB A:ASP53 4.4 12.4 1.0 C A:ASP53 4.4 13.0 1.0 N A:ASP53 4.4 12.9 1.0 O A:HOH389 4.4 18.9 1.0 CA A:ASP132 4.5 11.1 1.0 CA A:ASP53 4.6 11.8 1.0 MG A:MG404 4.7 14.3 1.0 CA A:ASP54 4.8 12.4 1.0 CE A:LYS133 4.9 12.2 1.0 CD A:LYS133 4.9 11.1 1.0 O A:ASP53 4.9 14.1 1.0 O A:LYS232 4.9 20.7 1.0 O A:HOH388 4.9 19.9 1.0 CG A:ASP12 4.9 14.9 1.0

Magnesium binding site 3 out of 3 in the Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Bifunctional Fructose 1,6-Bisphosphate Aldolase/Phosphatase (Aldolase Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:14.3 occ:1.00 O3P A:13P401 2.0 17.6 1.0 OD2 A:ASP53 2.1 14.2 1.0 O A:HOH387 2.1 16.4 1.0 OD2 A:ASP12 2.1 15.2 1.0 OE1 A:GLN95 2.2 17.1 1.0 ND1 A:HIS19 2.2 16.8 1.0 CE1 A:HIS19 3.0 19.1 1.0 CG A:ASP53 3.0 13.1 1.0 CG A:ASP12 3.1 14.9 1.0 CD A:GLN95 3.2 19.7 1.0 P A:13P401 3.3 17.3 1.0 CG A:HIS19 3.3 15.4 1.0 OD1 A:ASP12 3.5 15.7 1.0 NE2 A:GLN95 3.5 20.5 1.0 CB A:HIS19 3.8 12.9 1.0 O2P A:13P401 3.8 12.6 1.0 CB A:ASP53 3.8 12.4 1.0 OD1 A:ASP53 3.9 12.9 1.0 O A:HOH386 4.0 14.2 1.0 O1 A:13P401 4.0 19.2 1.0 CA A:HIS19 4.2 12.9 1.0 NE2 A:HIS19 4.2 18.8 1.0 OG A:SER15 4.2 14.1 1.0 CD2 A:HIS19 4.4 17.7 1.0 CB A:ASP12 4.4 14.6 1.0 O1P A:13P401 4.4 18.0 1.0 CG A:GLN95 4.5 18.7 1.0 MG A:MG403 4.7 12.1 1.0 C1 A:13P401 4.7 21.5 1.0 O A:HOH388 4.7 19.9 1.0 CB A:GLN95 4.9 19.2 1.0 CB A:ALA92 4.9 17.0 1.0

S.Fushinobu, H.Nishimasu, D.Hattori, H.-J.Song, T.Wakagi. Structural Basis For the Bifunctionality of Fructose-1,6-Bisphosphate Aldolase/Phosphatase. Nature V. 478 538 2011.
ISSN: ISSN 0028-0836
PubMed: 21983966
DOI: 10.1038/NATURE10457