Magnesium in PDB 4pb3: D-Threo-3-Hydroxyaspartate Dehydratase H351A Mutant

All present enzymatic activity of D-Threo-3-Hydroxyaspartate Dehydratase H351A Mutant:
4.3.1.27;

The structure of D-Threo-3-Hydroxyaspartate Dehydratase H351A Mutant, PDB code: 4pb3 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)	40.00 / 1.70
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.603, 157.603, 157.426, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.5

The binding sites of Magnesium atom in the D-Threo-3-Hydroxyaspartate Dehydratase H351A Mutant (pdb code 4pb3). 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 H351A Mutant, PDB code: 4pb3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the D-Threo-3-Hydroxyaspartate Dehydratase H351A Mutant


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 H351A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:14.2 occ:0.60 O B:HOH633 2.0 19.0 1.0 O A:HOH704 2.0 27.3 1.0 O A:HOH705 2.1 23.9 1.0 O A:HOH689 2.1 24.1 1.0 O A:HOH647 2.1 23.6 1.0 SG A:CYS353 3.6 24.7 1.0 O A:HOH628 3.8 19.0 1.0 O3P A:PLP401 4.0 20.5 1.0 OH A:TYR177 4.1 22.0 1.0 CB A:CYS353 4.1 14.5 1.0 OE1 B:GLN319 4.2 17.6 1.0 O A:HOH635 4.2 38.8 1.0 O B:HOH629 4.3 24.3 1.0 O B:HOH578 4.4 17.0 1.0 O A:HOH640 4.4 24.1 1.0 O A:HOH626 4.4 23.9 1.0 O B:HOH717 4.5 20.8 1.0 CE A:LYS43 4.5 17.3 1.0 CE2 A:TYR177 4.5 22.2 1.0 CZ A:TYR177 4.6 23.8 1.0 CZ2 B:TRP280 4.9 16.4 1.0

Magnesium binding site 2 out of 3 in the D-Threo-3-Hydroxyaspartate Dehydratase H351A Mutant


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 H351A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:11.8 occ:0.60 O B:HOH669 1.9 29.0 1.0 O A:HOH685 2.0 25.5 1.0 O A:HOH629 2.0 16.8 1.0 O B:HOH691 2.1 24.0 1.0 O B:HOH639 2.1 21.4 1.0 SG B:CYS353 3.5 25.1 1.0 O B:HOH607 3.7 21.4 1.0 O1P B:PLP401 3.9 20.1 1.0 OH B:TYR177 4.0 29.6 1.0 CB B:CYS353 4.1 15.4 1.0 OE1 A:GLN319 4.2 15.8 1.0 O A:HOH639 4.3 27.7 1.0 O B:HOH677 4.4 34.3 1.0 O B:HOH673 4.4 24.0 1.0 CE B:LYS43 4.4 16.1 1.0 O B:HOH608 4.4 23.6 1.0 O A:HOH588 4.5 15.9 1.0 CE2 B:TYR177 4.5 32.1 1.0 O B:HOH718 4.6 20.8 1.0 CZ B:TYR177 4.6 31.0 1.0 CZ2 A:TRP280 4.9 15.5 1.0 NZ B:LYS43 5.0 20.1 1.0

Magnesium binding site 3 out of 3 in the D-Threo-3-Hydroxyaspartate Dehydratase H351A Mutant


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 H351A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:17.1 occ:0.50 O A:HOH567 2.0 35.4 1.0 O B:HOH546 2.0 39.0 1.0 O B:HOH510 2.1 27.9 1.0 O A:HOH642 2.2 20.6 1.0 O B:HOH753 3.6 33.3 1.0 OXT B:TRP380 3.8 15.3 1.0 O B:HOH508 4.1 28.4 1.0 O B:TRP380 4.1 18.2 1.0 O B:HOH660 4.2 29.7 1.0 C B:TRP380 4.3 17.0 1.0 O A:HOH678 4.5 32.3 1.0 OD2 A:ASP9 4.5 20.5 1.0 NZ B:LYS68 4.5 18.6 0.5 CB A:ASP9 4.7 16.0 1.0 O B:HOH543 4.8 32.6 1.0

Y.Matsumoto, Y.Yasutake, Y.Takeda, T.Tamura, A.Yokota, M.Wada. Structure of D-Threo-3-Hydroxyaspartate Dehydratase To Be Published.