Magnesium in PDB 1dxf: 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate

All present enzymatic activity of 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate:
4.1.2.20;

The structure of 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate, PDB code: 1dxf was solved by T.Izard, N.C.Blackwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20 / 2.6
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	126.400, 126.400, 172.000, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 23.3

The binding sites of Magnesium atom in the 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate (pdb code 1dxf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate, PDB code: 1dxf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:21.1 occ:1.00 OE1 A:GLU153 2.3 38.5 1.0 OD2 A:ASP179 2.3 42.4 1.0 O A:HOH2027 2.4 36.1 1.0 O3 A:PYR501 2.5 44.2 1.0 O1 A:PYR501 2.6 44.2 1.0 OE2 A:GLU153 2.9 38.5 1.0 CD A:GLU153 2.9 38.5 1.0 C2 A:PYR501 3.2 44.2 1.0 C1 A:PYR501 3.2 44.2 1.0 CG A:ASP179 3.4 42.4 1.0 CB A:ASP179 3.8 42.4 1.0 OE1 A:GLN151 3.8 40.7 1.0 OE1 A:GLU49 4.2 36.6 1.0 CG A:GLU153 4.4 38.5 1.0 O2 A:PYR501 4.4 44.2 1.0 OD1 A:ASP179 4.4 42.4 1.0 NE2 A:HIS50 4.4 27.2 1.0 C3 A:PYR501 4.6 44.2 1.0 CD2 A:HIS50 4.6 27.2 1.0 NH1 A:ARG75 4.7 34.1 1.0 O A:HOH2043 4.7 19.9 1.0 CD A:GLN151 4.7 40.7 1.0 CE2 A:PHE99 4.8 34.6 1.0 CB A:GLU153 4.9 38.5 1.0 CA A:GLY176 4.9 33.8 1.0 CZ A:PHE99 4.9 34.6 1.0 CD A:GLU49 5.0 36.6 1.0 OE2 A:GLU49 5.0 36.6 1.0 N A:ASP179 5.0 40.1 1.0 CZ A:ARG75 5.0 34.1 1.0

Magnesium binding site 2 out of 2 in the 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2-Dehydro-3-Deoxy-Galactarate Aldolase From Escherichia Coli in Complex with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:20.4 occ:1.00 O B:HOH2034 2.3 24.9 1.0 OD2 B:ASP179 2.3 37.1 1.0 OE1 B:GLU153 2.3 39.3 1.0 O3 B:PYR501 2.5 49.0 1.0 O1 B:PYR501 2.7 49.0 1.0 CD B:GLU153 3.2 39.3 1.0 C2 B:PYR501 3.3 49.0 1.0 C1 B:PYR501 3.3 49.0 1.0 CG B:ASP179 3.3 37.1 1.0 O B:HOH2105 3.4 39.5 1.0 OE2 B:GLU153 3.6 39.3 1.0 CB B:ASP179 3.7 37.1 1.0 OE1 B:GLN151 3.8 45.4 1.0 O B:HOH2046 4.3 14.2 1.0 OE1 B:GLU49 4.3 35.3 1.0 OD1 B:ASP179 4.4 37.1 1.0 O2 B:PYR501 4.5 49.0 1.0 CG B:GLU153 4.5 39.3 1.0 CE1 B:HIS50 4.7 34.9 1.0 NH1 B:ARG75 4.7 34.4 1.0 N B:ASP179 4.7 38.3 1.0 CA B:GLY176 4.7 29.7 1.0 CB B:GLU153 4.7 39.3 1.0 C3 B:PYR501 4.7 49.0 1.0 CD B:GLN151 4.8 45.4 1.0 CA B:ASP179 4.9 38.3 1.0

T.Izard, N.C.Blackwell. Crystal Structures of the Metal-Dependent 2-Dehydro-3-Deoxy-Galactarate Aldolase Suggest A Novel Reaction Mechanism. Embo J. V. 19 3849 2000.
ISSN: ISSN 0261-4189
PubMed: 10921867
DOI: 10.1093/EMBOJ/19.15.3849