Magnesium in PDB 2q1d: 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2,5-Dioxopentanoate

The structure of 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2,5-Dioxopentanoate, PDB code: 2q1d 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)	19.58 / 2.70
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.280, 128.280, 223.520, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26.1

The binding sites of Magnesium atom in the 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2,5-Dioxopentanoate (pdb code 2q1d). 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 2,5-Dioxopentanoate, PDB code: 2q1d:

Magnesium binding site 1 out of 1 in the 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed with Magnesium and 2,5-Dioxopentanoate


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 2,5-Dioxopentanoate within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg294 b:34.2 occ:1.00 OD2 X:ASP164 1.9 39.1 1.0 O X:HOH898 2.0 36.8 1.0 O5 X:DO4897 2.1 52.5 1.0 OE1 X:GLU145 2.2 43.0 1.0 O2 X:DO4897 2.2 49.9 1.0 OE2 X:GLU143 2.3 47.0 1.0 C2 X:DO4897 2.9 52.0 1.0 C1 X:DO4897 2.9 51.3 1.0 CG X:ASP164 3.1 38.7 1.0 CD X:GLU145 3.2 43.5 1.0 NZ X:LYS182 3.4 37.1 1.0 CD X:GLU143 3.5 45.1 1.0 OE2 X:GLU145 3.6 42.8 1.0 CB X:ASP164 3.6 38.1 1.0 O X:SER79 4.1 50.8 1.0 OD1 X:ASP164 4.1 37.8 1.0 CB X:GLU143 4.2 44.4 1.0 O1 X:DO4897 4.2 50.9 1.0 CZ X:PHE116 4.2 42.8 1.0 C3 X:DO4897 4.3 53.2 1.0 CA X:GLY255 4.3 46.5 1.0 OE1 X:GLU143 4.3 44.8 1.0 N X:THR256 4.4 47.8 1.0 CG X:GLU143 4.4 44.5 1.0 CG X:GLU145 4.5 42.4 1.0 CE2 X:PHE116 4.6 41.7 1.0 CE X:LYS182 4.7 36.0 1.0 C4 X:DO4897 4.7 55.3 1.0 CG2 X:THR256 4.8 48.1 1.0 C X:GLY255 4.8 47.3 1.0 CB X:THR256 4.9 48.2 1.0 O X:ASP164 4.9 39.0 1.0 OG X:SER166 4.9 44.2 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