Magnesium in PDB 2q1a: 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2-Oxobutyrate

The structure of 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2-Oxobutyrate, PDB code: 2q1a was solved by T.Barends, S.Brouns, P.Worm, J.Akerboom, A.Turnbull, L.Salmon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.66 / 2.50
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.830, 128.830, 224.400, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 25.6

The binding sites of Magnesium atom in the 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2-Oxobutyrate (pdb code 2q1a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2-Oxobutyrate, PDB code: 2q1a:

Magnesium binding site 1 out of 1 in the 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2-Oxobutyrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2-Oxobutyrate within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg294 b:26.4 occ:1.00 OD2 X:ASP164 2.0 32.7 1.0 OE1 X:GLU145 2.0 36.3 1.0 OE2 X:GLU143 2.1 37.2 1.0 O X:HOH326 2.2 34.1 1.0 O3 X:2KT295 2.2 33.8 1.0 O2 X:2KT295 2.4 33.2 1.0 C2 X:2KT295 3.0 33.5 1.0 CG X:ASP164 3.1 32.4 1.0 C1 X:2KT295 3.1 33.2 1.0 CD X:GLU145 3.2 36.4 1.0 CD X:GLU143 3.3 38.0 1.0 NZ X:LYS182 3.4 30.3 1.0 CB X:ASP164 3.5 33.0 1.0 OE2 X:GLU145 3.7 36.0 1.0 CB X:GLU143 4.0 37.9 1.0 OE1 X:GLU143 4.1 36.9 1.0 OD1 X:ASP164 4.2 31.1 1.0 C3 X:2KT295 4.3 33.6 1.0 CG X:GLU143 4.3 37.9 1.0 O1 X:2KT295 4.4 33.4 1.0 O X:SER79 4.4 47.2 1.0 CG X:GLU145 4.4 36.0 1.0 N X:THR256 4.4 43.9 1.0 CZ X:PHE116 4.5 34.9 1.0 CA X:GLY255 4.5 42.6 1.0 C4 X:2KT295 4.6 32.9 1.0 CG2 X:THR256 4.7 44.5 1.0 O X:ASP164 4.8 33.7 1.0 NH1 X:ARG89 4.8 85.2 1.0 CB X:THR256 4.8 44.6 1.0 C X:GLY255 4.9 43.3 1.0 CE X:LYS182 4.9 30.3 1.0 CA X:ASP164 4.9 33.3 1.0 OG X:SER166 5.0 36.2 1.0 CE2 X:PHE116 5.0 35.7 1.0

S.J.Brouns, T.R.Barends, P.Worm, J.Akerboom, A.P.Turnbull, L.Salmon, J.Van Der Oost. Structural Insight Into Substrate Binding and Catalysis of A Novel 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Illustrates Common Mechanistic Features of the Fah Superfamily. J.Mol.Biol. V. 379 357 2008.
ISSN: ISSN 0022-2836
PubMed: 18448118
DOI: 10.1016/J.JMB.2008.03.064