Magnesium in PDB 3wqe: D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine

All present enzymatic activity of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine:
4.3.1.27;

The structure of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine, PDB code: 3wqe was solved by Y.Yasutake, Y.Matsumoto, M.Wada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.33 / 1.60
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.978, 157.978, 158.860, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.2

The binding sites of Magnesium atom in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine (pdb code 3wqe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine, PDB code: 3wqe:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:11.9 occ:0.50 NE2 A:HIS351 2.1 15.5 1.0 O A:HOH712 2.1 20.7 1.0 O A:HOH674 2.1 19.8 1.0 O B:HOH614 2.1 19.1 1.0 O A:HOH711 2.3 27.8 1.0 SG A:CYS353 2.7 16.3 1.0 CE1 A:HIS351 3.0 15.0 1.0 CD2 A:HIS351 3.2 16.7 1.0 CB A:CYS353 3.5 11.8 1.0 NZ A:LYS43 3.7 24.9 1.0 OH A:TYR177 4.0 19.2 1.0 O3P A:PLP401 4.2 18.1 1.0 ND1 A:HIS351 4.3 15.7 1.0 OE1 B:GLN319 4.3 15.4 1.0 CG A:HIS351 4.3 13.8 1.0 O A:HOH530 4.4 17.0 1.0 CA A:2TL403 4.5 17.8 1.0 OXT A:2TL403 4.5 17.6 1.0 O B:HOH704 4.5 26.1 1.0 CB A:VAL237 4.6 11.4 1.0 CG2 A:VAL237 4.7 11.6 1.0 CE2 A:TYR177 4.7 18.4 1.0 CZ A:TYR177 4.8 19.1 1.0 O A:HOH615 4.8 23.1 1.0 O A:HOH553 4.8 22.4 1.0 CA A:CYS353 4.9 11.1 1.0 N A:CYS353 4.9 10.9 1.0 O A:HOH572 4.9 19.4 1.0 C A:2TL403 5.0 18.7 1.0

Magnesium binding site 2 out of 3 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:19.8 occ:1.00 O B:HOH611 2.0 18.4 1.0 O B:HOH629 2.0 22.2 1.0 O A:HOH619 2.1 16.8 1.0 NE2 B:HIS351 2.1 15.3 1.0 O B:HOH633 2.3 25.3 1.0 SG B:CYS353 2.6 17.4 1.0 CD2 B:HIS351 3.2 17.5 1.0 CE1 B:HIS351 3.2 16.0 1.0 CB B:CYS353 3.5 13.5 1.0 NZ B:LYS43 3.6 25.8 1.0 OH B:TYR177 4.0 19.4 1.0 O3P B:PLP401 4.2 18.9 1.0 OE1 A:GLN319 4.3 14.0 1.0 ND1 B:HIS351 4.4 16.1 1.0 CG B:HIS351 4.4 15.2 1.0 CA B:2TL403 4.5 15.7 1.0 O B:HOH535 4.5 18.3 1.0 O B:HOH672 4.5 26.8 1.0 OXT B:2TL403 4.5 15.0 1.0 CB B:VAL237 4.6 14.8 1.0 CE2 B:TYR177 4.7 20.2 1.0 CG2 B:VAL237 4.7 15.3 1.0 CZ B:TYR177 4.8 19.9 1.0 CA B:CYS353 4.8 12.9 1.0 O B:HOH546 4.8 20.2 1.0 O B:HOH558 4.9 18.4 1.0 O B:HOH544 4.9 20.6 1.0 N B:CYS353 4.9 12.9 1.0 C B:2TL403 5.0 16.4 1.0

Magnesium binding site 3 out of 3 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Allothreonine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:17.1 occ:0.50 O B:HOH642 2.0 25.3 1.0 O A:HOH774 2.0 39.3 1.0 O B:HOH631 2.0 28.7 1.0 O B:HOH761 2.0 35.1 1.0 O B:HOH762 2.1 30.7 1.0 O A:HOH600 2.2 21.9 1.0 O A:HOH665 3.7 28.6 1.0 OXT B:TRP380 3.8 14.1 1.0 O B:HOH701 3.9 29.3 1.0 O B:HOH763 4.0 34.4 1.0 O B:TRP380 4.1 16.0 1.0 O B:HOH647 4.2 29.0 1.0 C B:TRP380 4.3 13.6 1.0 O A:HOH679 4.5 30.2 1.0 OD2 A:ASP9 4.6 20.6 1.0 NZ B:LYS68 4.7 19.4 0.5 O B:HOH719 4.7 29.4 1.0 CB A:ASP9 4.8 14.6 1.0

Y.Matsumoto, Y.Yasutake, Y.Takeda, T.Tamura, A.Yokota, M.Wada. Structutal Insights Into Substrate Stereo-Specificity of D-Threo-3-Hydroxyaspartate Dehydratase To Be Published.