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Magnesium in PDB 3wqc: D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23

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

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

Protein crystallography data

The structure of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23, PDB code: 3wqc 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) 45.63 / 1.50
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 157.689, 157.689, 158.784, 90.00, 90.00, 90.00
R / Rfree (%) 12.1 / 15.2

Other elements in 3wqc:

The structure of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23 (pdb code 3wqc). 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, PDB code: 3wqc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3wqc

Go back to Magnesium Binding Sites List in 3wqc
Magnesium binding site 1 out of 5 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:14.1
occ:1.00
 O A:HOH696 2.1 18.0 1.0
O A:HOH565 2.1 14.1 1.0
NE2 A:HIS351 2.1 11.9 1.0
O B:HOH579 2.2 15.1 1.0
O A:HOH560 2.2 19.5 1.0
SG A:CYS353 2.6 14.1 1.0
CE1 A:HIS351 3.1 12.7 1.0
CD2 A:HIS351 3.2 11.2 1.0
CB A:CYS353 3.5 12.8 1.0
OH A:TYR177 4.2 17.4 1.0
C1 A:GOL404 4.2 36.0 1.0
O3P A:PLP401 4.3 19.8 1.0
O1 A:GOL404 4.3 54.1 1.0
ND1 A:HIS351 4.3 12.4 1.0
CG A:HIS351 4.3 10.7 1.0
OE1 B:GLN319 4.4 13.9 1.0
O A:HOH520 4.4 14.7 1.0
O A:HOH648 4.5 26.8 1.0
CL B:CL401 4.6 19.7 0.7
CB A:VAL237 4.7 11.2 1.0
O A:HOH564 4.7 21.0 1.0
CE2 A:TYR177 4.7 16.6 1.0
CG2 A:VAL237 4.8 12.6 1.0
O B:HOH520 4.8 20.0 1.0
CA A:CYS353 4.8 10.6 1.0
CZ A:TYR177 4.9 16.9 1.0
N A:CYS353 4.9 10.4 1.0
CE A:LYS43 4.9 23.0 1.0
O A:HOH584 5.0 20.1 1.0

Magnesium binding site 2 out of 5 in 3wqc

Go back to Magnesium Binding Sites List in 3wqc
Magnesium binding site 2 out of 5 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:28.2
occ:0.50
 O A:HOH672 1.7 52.9 1.0
O A:HOH739 1.8 48.6 1.0
O B:HOH605 2.2 24.7 1.0
O A:HOH738 2.4 39.9 1.0
OXT A:TRP380 2.4 16.1 1.0
C A:TRP380 3.4 16.8 1.0
O A:TRP380 3.6 22.1 1.0
O A:HOH524 4.2 16.4 1.0
NE2 A:GLN94 4.2 24.5 0.5
OE1 A:GLN94 4.2 40.6 0.5
OE1 A:GLN94 4.2 20.3 0.5
OD2 B:ASP9 4.3 24.1 1.0
O B:HOH649 4.5 37.4 1.0
CD A:GLN94 4.6 20.2 0.5
CA A:TRP380 4.7 12.6 1.0
CB A:LYS68 4.8 12.8 1.0

Magnesium binding site 3 out of 5 in 3wqc

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:14.8
occ:1.00
 O B:HOH577 2.1 15.1 1.0
O B:HOH707 2.1 20.0 1.0
O A:HOH557 2.1 14.8 1.0
NE2 B:HIS351 2.1 12.7 1.0
O B:HOH562 2.2 20.4 1.0
SG B:CYS353 2.6 15.1 1.0
CE1 B:HIS351 3.2 13.8 1.0
CD2 B:HIS351 3.2 13.5 1.0
CB B:CYS353 3.5 13.6 1.0
O B:HOH807 4.0 47.4 1.0
OH B:TYR177 4.1 18.2 1.0
O3P B:PLP402 4.3 19.3 1.0
OE1 A:GLN319 4.3 13.2 1.0
ND1 B:HIS351 4.3 12.2 1.0
CG B:HIS351 4.3 12.2 1.0
O B:HOH538 4.4 16.4 1.0
O A:HOH660 4.6 27.5 1.0
CL A:CL405 4.6 19.0 0.7
CB B:VAL237 4.7 13.2 1.0
O B:HOH539 4.7 20.4 1.0
CG2 B:VAL237 4.8 15.3 1.0
CE2 B:TYR177 4.8 16.9 1.0
CE B:LYS43 4.8 23.8 1.0
CA B:CYS353 4.8 12.1 1.0
CZ B:TYR177 4.8 16.2 1.0
O A:HOH526 4.8 20.9 1.0
N B:CYS353 4.9 12.3 1.0
O B:HOH581 5.0 17.8 1.0

Magnesium binding site 4 out of 5 in 3wqc

Go back to Magnesium Binding Sites List in 3wqc
Magnesium binding site 4 out of 5 in the D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. HT23


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:37.6
occ:1.00
 O B:HOH711 2.0 40.0 1.0
O A:HOH701 2.1 37.5 1.0
O A:HOH700 2.2 44.9 1.0
O A:HOH622 2.2 28.0 1.0
O B:HOH710 2.2 37.9 1.0
O A:HOH699 2.3 43.0 1.0
OD2 A:ASP136 3.8 28.8 1.0
OD2 B:ASP270 4.0 56.4 1.0
OE1 B:GLN268 4.1 29.1 1.0
O B:HOH692 4.3 38.2 1.0
OD1 B:ASP270 4.3 44.0 1.0
CA A:GLY145 4.4 26.1 1.0
O A:HOH777 4.5 51.9 1.0
O A:HOH613 4.6 34.0 1.0
CG B:ASP270 4.6 32.7 1.0
CG A:ASP136 4.8 22.2 1.0
N A:GLY145 4.8 25.9 1.0
O B:HOH770 4.9 45.1 1.0
CD B:GLN268 4.9 20.7 1.0

Magnesium binding site 5 out of 5 in 3wqc

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:21.4
occ:0.50
 O A:HOH801 2.0 39.9 1.0
O B:HOH634 2.0 28.9 1.0
O A:HOH817 2.1 29.0 0.5
O B:HOH768 2.1 39.9 1.0
O A:HOH601 2.2 21.2 1.0
O A:HOH705 3.8 35.4 1.0
O B:HOH810 3.8 26.6 0.5
OXT B:TRP380 3.9 13.7 1.0
O B:HOH718 3.9 36.3 1.0
O B:TRP380 4.1 18.5 1.0
O B:HOH716 4.2 29.7 1.0
C B:TRP380 4.4 14.1 1.0
O A:HOH641 4.4 38.0 1.0
OD2 A:ASP9 4.6 21.9 1.0
NZ B:LYS68 4.7 24.0 0.5
CB A:ASP9 4.7 12.6 1.0
O B:HOH717 4.9 41.6 1.0

Reference:

Y.Matsumoto, Y.Yasutake, Y.Takeda, T.Tamura, A.Yokota, M.Wada. Structural Insights Into Substrate Stereo-Specificity of D-Threo-3-Hydroxyaspartate Dehydratase To Be Published.
Page generated: Mon Aug 11 04:56:01 2025

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