Magnesium in PDB 3bqb: Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase

The structure of Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase, PDB code: 3bqb was solved by T.M.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)	33.74 / 2.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	157.092, 157.092, 131.921, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 28.4

The binding sites of Magnesium atom in the Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase (pdb code 3bqb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase, PDB code: 3bqb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg294 b:82.8 occ:1.00 OE2 A:GLU143 2.3 61.8 1.0 OE1 A:GLU145 2.4 59.1 1.0 OD2 A:ASP164 2.6 56.9 1.0 NZ A:LYS182 3.2 54.6 1.0 CG A:ASP164 3.5 56.7 1.0 CD A:GLU143 3.5 60.4 1.0 CD A:GLU145 3.5 59.3 1.0 CB A:ASP164 3.8 56.6 1.0 OE2 A:GLU145 3.9 60.0 1.0 CZ A:PHE116 4.1 57.2 1.0 OE1 A:GLU143 4.2 60.7 1.0 CB A:GLU143 4.4 60.1 1.0 OD1 A:ASP164 4.4 57.1 1.0 CE A:LYS182 4.5 54.3 1.0 CA A:GLY255 4.5 63.1 1.0 CG A:GLU143 4.5 60.2 1.0 CE2 A:PHE116 4.7 57.1 1.0 N A:THR256 4.8 63.9 1.0 OG A:SER166 4.8 57.3 1.0 CG A:GLU145 4.8 59.4 1.0

Magnesium binding site 2 out of 4 in the Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg294 b:73.4 occ:1.00 OE1 X:GLU145 2.3 56.1 1.0 OD2 X:ASP164 2.3 53.5 1.0 OE2 X:GLU143 2.7 59.8 1.0 CD X:GLU145 3.2 55.5 1.0 CG X:ASP164 3.4 53.1 1.0 OE2 X:GLU145 3.4 55.4 1.0 NZ X:LYS182 3.7 55.2 1.0 CZ X:PHE116 3.8 54.3 1.0 CB X:ASP164 3.8 53.1 1.0 CD X:GLU143 4.0 58.4 1.0 CE2 X:PHE116 4.3 54.2 1.0 CA X:GLY255 4.3 56.0 1.0 OD1 X:ASP164 4.4 52.8 1.0 CG X:GLU145 4.6 55.5 1.0 CB X:GLU143 4.7 57.9 1.0 N X:THR256 4.7 57.1 1.0 CE X:LYS182 4.7 55.2 1.0 OE1 X:GLU143 4.7 60.2 1.0 CA X:GLY80 4.8 63.0 1.0 C X:GLY255 4.8 56.5 1.0 O X:SER79 4.9 61.7 1.0 N X:GLY255 4.9 55.6 1.0 CG2 X:THR253 4.9 52.9 1.0 CE1 X:PHE116 4.9 54.4 1.0 CG X:GLU143 5.0 58.2 1.0

Magnesium binding site 3 out of 4 in the Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg294 b:88.6 occ:1.00 OE1 Z:GLU145 2.3 65.8 1.0 OE2 Z:GLU143 2.3 66.7 1.0 OD2 Z:ASP164 2.5 64.3 1.0 CD Z:GLU145 3.4 65.4 1.0 CG Z:ASP164 3.5 64.4 1.0 NZ Z:LYS182 3.5 59.3 1.0 CD Z:GLU143 3.6 66.2 1.0 CB Z:ASP164 3.8 64.3 1.0 OE2 Z:GLU145 3.8 65.1 1.0 OE1 Z:GLU143 4.3 66.4 1.0 CB Z:GLU143 4.3 66.2 1.0 CZ Z:PHE116 4.4 65.9 1.0 OD1 Z:ASP164 4.5 65.4 1.0 CG Z:GLU143 4.6 66.0 1.0 CA Z:GLY255 4.6 70.0 1.0 N Z:THR256 4.6 70.8 1.0 CG Z:GLU145 4.7 65.4 1.0 CG2 Z:THR256 4.7 70.9 1.0 CE2 Z:PHE116 4.8 65.9 1.0 CE Z:LYS182 4.8 59.7 1.0 O Z:SER79 4.8 69.8 1.0 CA Z:GLY80 4.9 71.3 1.0

Magnesium binding site 4 out of 4 in the Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hexagonal Kristal Form of 2-Keto-3-Deoxyarabinonate Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg294 b:88.4 occ:1.00 OE2 Y:GLU143 2.2 64.7 1.0 OE1 Y:GLU145 2.5 60.2 1.0 OD2 Y:ASP164 2.9 61.3 1.0 CD Y:GLU143 3.4 65.0 1.0 NZ Y:LYS182 3.5 64.2 1.0 CD Y:GLU145 3.6 60.7 1.0 CG Y:ASP164 3.9 60.7 1.0 OE2 Y:GLU145 4.0 59.9 1.0 OE1 Y:GLU143 4.1 65.1 1.0 O Y:SER79 4.2 65.6 1.0 CZ Y:PHE116 4.2 62.8 1.0 CB Y:ASP164 4.3 60.8 1.0 CB Y:GLU143 4.5 65.0 1.0 CE2 Y:PHE116 4.5 62.9 1.0 CG Y:GLU143 4.6 64.9 1.0 N Y:THR256 4.6 66.8 1.0 CA Y:GLY255 4.6 65.3 1.0 CE Y:LYS182 4.7 64.3 1.0 CG2 Y:THR256 4.7 67.5 1.0 CA Y:GLY80 4.8 67.1 1.0 CG Y:GLU145 4.8 60.9 1.0 OD1 Y:ASP164 4.9 60.5 1.0 C Y:SER79 5.0 65.4 1.0 C Y:GLY255 5.0 66.0 1.0

S.J.J.Brouns, T.R.M.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