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

Enzymatic activity of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate

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

Protein crystallography data

The structure of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate, PDB code: 3wqd 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) 28.88 / 1.50
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 157.834, 157.834, 158.217, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate (pdb code 3wqd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate, PDB code: 3wqd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3wqd

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Magnesium binding site 1 out of 5 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate


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-Erythro-3-Hydroxyaspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.8
occ:1.00
 O A:HOH603 2.1 18.7 1.0
O A:HOH611 2.1 17.5 1.0
O B:HOH566 2.1 17.2 1.0
NE2 A:HIS351 2.1 17.2 1.0
OD1 A:999403 2.1 18.1 1.0
SG A:CYS353 2.7 17.5 1.0
CE1 A:HIS351 3.1 17.7 1.0
CD2 A:HIS351 3.2 15.2 1.0
CG A:999403 3.3 17.9 1.0
CB A:CYS353 3.7 16.2 1.0
OH A:TYR177 4.0 18.0 1.0
CA A:999403 4.0 18.6 1.0
CB A:999403 4.0 19.6 1.0
ND1 A:HIS351 4.3 15.9 1.0
OXT A:999403 4.3 19.3 1.0
OD2 A:999403 4.3 21.7 1.0
OE1 B:GLN319 4.4 16.1 1.0
CG A:HIS351 4.4 13.1 1.0
O3P A:PLP401 4.4 20.8 1.0
O A:HOH515 4.4 17.7 1.0
CE2 A:TYR177 4.5 18.3 1.0
CB A:VAL237 4.6 15.1 1.0
C A:999403 4.7 18.8 1.0
CZ A:TYR177 4.7 17.5 1.0
CG2 A:VAL237 4.8 14.8 1.0
CE A:LYS43 4.9 22.1 1.0
O A:HOH525 4.9 20.9 1.0
O A:HOH600 4.9 21.5 1.0
O B:HOH553 4.9 21.9 1.0
CA A:CYS353 5.0 13.4 1.0
N A:CYS353 5.0 11.6 1.0

Magnesium binding site 2 out of 5 in 3wqd

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Magnesium binding site 2 out of 5 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate


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-Erythro-3-Hydroxyaspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:23.6
occ:0.50
 O A:HOH581 1.8 29.9 1.0
O B:HOH736 2.0 34.9 0.5
OD2 A:999403 2.1 21.7 1.0
OB A:999403 2.1 21.1 1.0
OD1 B:ASN318 2.3 33.1 0.5
CE1 A:HIS140 2.9 34.6 1.0
CG A:999403 3.0 17.9 1.0
NE2 A:HIS140 3.0 40.2 1.0
CB A:999403 3.1 19.6 1.0
CG B:ASN318 3.4 30.5 0.5
OD1 B:ASN318 3.4 27.9 0.5
CG B:ASN318 3.6 27.9 0.5
ND2 B:ASN318 3.6 20.0 0.5
ND2 B:ASN318 4.0 36.5 0.5
O B:HOH755 4.0 48.2 1.0
O B:HOH553 4.1 21.9 1.0
O A:HOH600 4.2 21.5 1.0
C A:999403 4.2 18.8 1.0
OD1 A:999403 4.2 18.1 1.0
CA A:999403 4.2 18.6 1.0
ND1 A:HIS140 4.2 40.7 1.0
CD2 A:HIS140 4.3 32.4 1.0
O A:GLY174 4.3 22.3 1.0
OXT A:999403 4.4 19.3 1.0
NE2 A:HIS172 4.4 19.0 1.0
CB B:ASN318 4.5 19.8 0.5
CB B:ASN318 4.6 22.1 0.5
CA A:GLY174 4.6 21.8 1.0
O A:999403 4.6 22.7 1.0
NH1 A:ARG141 4.6 23.7 1.0
CD2 A:TYR177 4.8 17.9 1.0
C A:GLY174 4.8 22.3 1.0
CE2 A:TYR177 4.9 18.3 1.0
CG A:TYR177 4.9 18.7 1.0
CG A:HIS140 4.9 28.2 1.0
O B:HOH744 4.9 38.6 1.0
N A:999403 4.9 19.7 1.0

Magnesium binding site 3 out of 5 in 3wqd

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Magnesium binding site 3 out of 5 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate


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-Erythro-3-Hydroxyaspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:18.2
occ:1.00
 O B:HOH595 2.1 18.0 1.0
O B:HOH588 2.1 19.7 1.0
O A:HOH563 2.1 16.2 1.0
OD1 B:999405 2.1 19.6 1.0
NE2 B:HIS351 2.1 16.8 1.0
SG B:CYS353 2.7 18.1 1.0
CE1 B:HIS351 3.2 17.2 1.0
CD2 B:HIS351 3.2 17.3 1.0
CG B:999405 3.3 18.0 1.0
CB B:CYS353 3.6 16.4 1.0
NZ B:LYS43 3.8 34.6 1.0
OH B:TYR177 4.0 19.0 1.0
CB B:999405 4.0 17.7 1.0
CA B:999405 4.0 17.5 1.0
OXT B:999405 4.3 16.8 1.0
OE1 A:GLN319 4.3 15.8 1.0
OD2 B:999405 4.3 20.9 1.0
ND1 B:HIS351 4.3 15.3 1.0
O3P B:PLP402 4.4 19.8 1.0
CG B:HIS351 4.4 13.7 1.0
O B:HOH540 4.4 18.7 1.0
CE2 B:TYR177 4.6 19.0 1.0
CB B:VAL237 4.6 16.9 1.0
C B:999405 4.7 18.1 1.0
CZ B:TYR177 4.7 16.4 1.0
CG2 B:VAL237 4.8 17.9 1.0
O B:HOH582 4.9 22.1 1.0
O B:HOH713 4.9 21.0 1.0
CA B:CYS353 4.9 14.7 1.0
N B:CYS353 5.0 14.7 1.0
O A:HOH547 5.0 19.4 1.0

Magnesium binding site 4 out of 5 in 3wqd

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Magnesium binding site 4 out of 5 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:22.1
occ:0.50
 O B:HOH735 1.9 44.7 1.0
O B:HOH677 1.9 28.0 1.0
OD2 B:999405 2.1 20.9 1.0
OB B:999405 2.1 18.6 1.0
CE1 B:HIS140 2.7 24.9 1.0
CG B:999405 2.9 18.0 1.0
NE2 B:HIS140 3.0 32.5 1.0
CB B:999405 3.1 17.7 1.0
ND2 A:ASN318 3.5 32.9 1.0
CG A:ASN318 3.7 23.5 1.0
OD1 A:ASN318 3.9 28.4 1.0
O A:HOH720 3.9 37.5 1.0
O A:HOH547 4.1 19.4 1.0
C B:999405 4.1 18.1 1.0
ND1 B:HIS140 4.1 31.7 1.0
CA B:999405 4.1 17.5 1.0
OD1 B:999405 4.1 19.6 1.0
O B:HOH582 4.2 22.1 1.0
OXT B:999405 4.3 16.8 1.0
CD2 B:HIS140 4.3 22.6 1.0
NE2 B:HIS172 4.4 17.5 1.0
O B:GLY174 4.4 21.0 1.0
O B:999405 4.5 18.2 1.0
CB A:ASN318 4.5 14.5 1.0
O B:HOH804 4.6 46.2 1.0
CA B:GLY174 4.6 20.0 1.0
CD2 B:TYR177 4.7 19.0 1.0
O A:HOH622 4.7 35.1 1.0
NH1 B:ARG141 4.7 19.1 1.0
CE2 B:TYR177 4.8 19.0 1.0
N B:999405 4.9 17.9 1.0
CG B:HIS140 4.9 26.2 1.0
C B:GLY174 4.9 20.8 1.0
CG B:TYR177 4.9 18.2 1.0

Magnesium binding site 5 out of 5 in 3wqd

Go back to Magnesium Binding Sites List in 3wqd
Magnesium binding site 5 out of 5 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 Complexed with D-Erythro-3-Hydroxyaspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:23.3
occ:0.50
 O B:HOH697 2.0 34.9 1.0
O A:HOH615 2.2 26.3 1.0
O B:HOH651 2.4 38.9 1.0
OXT B:TRP380 3.8 15.1 1.0
O A:HOH683 3.8 35.4 1.0
O B:HOH704 3.9 36.3 1.0
O B:HOH644 4.0 38.8 1.0
O B:HOH820 4.0 36.3 1.0
O B:TRP380 4.1 19.7 1.0
C B:TRP380 4.3 15.7 1.0
O A:HOH794 4.3 37.2 1.0
O A:HOH639 4.5 36.1 1.0
OD2 A:ASP9 4.6 24.7 1.0
NZ B:LYS68 4.7 26.2 0.5
CB A:ASP9 4.8 16.0 1.0
O B:HOH719 4.8 33.9 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: Mon Aug 11 04:58:57 2025

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