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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 3wqe

Go back to Magnesium Binding Sites List in 3wqe
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 3wqe

Go back to Magnesium Binding Sites List in 3wqe
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 3wqe

Go back to Magnesium Binding Sites List in 3wqe
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

Reference:

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.
Page generated: Thu Aug 15 13:33:21 2024

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