Magnesium in PDB 5ti1: Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400

Enzymatic activity of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400

All present enzymatic activity of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400:
3.7.1.2;

Protein crystallography data

The structure of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400, PDB code: 5ti1 was solved by Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.31 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.900, 83.100, 186.290, 101.63, 91.17, 113.81
R / Rfree (%) 15.4 / 19.9

Other elements in 5ti1:

The structure of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 (pdb code 5ti1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400, PDB code: 5ti1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5ti1

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Magnesium binding site 1 out of 8 in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:28.8
occ:1.00
 OE2 A:GLU218 2.2 40.2 1.0
OD2 A:ASP145 2.2 31.6 1.0
OE1 A:GLU220 2.3 31.9 1.0
OD2 A:ASP252 2.3 32.3 1.0
O A:HOH784 2.6 32.5 1.0
CG A:ASP252 3.3 33.2 1.0
CG A:ASP145 3.3 30.6 1.0
NZ A:LYS272 3.4 34.2 1.0
CD A:GLU220 3.4 32.7 1.0
CD A:GLU218 3.4 36.8 1.0
CB A:ASP252 3.5 25.9 1.0
OH A:TYR178 3.7 28.4 1.0
OD1 A:ASP145 3.8 31.5 1.0
O A:HOH691 3.9 34.7 1.0
O A:HOH793 3.9 43.4 1.0
OE2 A:GLU220 3.9 26.7 1.0
CB A:GLU218 4.2 27.4 1.0
OE1 A:GLU218 4.3 34.7 1.0
CG A:GLU218 4.3 31.6 1.0
CE A:LYS272 4.4 40.7 1.0
OD1 A:ASP252 4.4 39.9 1.0
CB A:ASP145 4.6 18.2 1.0
CG A:GLU220 4.6 27.1 1.0
OG1 A:THR369 4.7 29.4 1.0
CA A:GLY368 4.7 29.0 1.0
O A:PHE146 4.7 25.0 1.0
CZ A:TYR178 4.8 29.9 1.0
N A:THR369 4.8 28.2 1.0
CE1 A:TYR178 4.8 32.7 1.0
O A:ASP252 4.9 21.9 1.0
O A:HOH659 4.9 32.5 1.0
CA A:ASP252 4.9 24.7 1.0

Magnesium binding site 2 out of 8 in 5ti1

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Magnesium binding site 2 out of 8 in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:29.0
occ:1.00
 OE2 B:GLU218 2.2 39.6 1.0
OE1 B:GLU220 2.2 27.2 1.0
OD2 B:ASP145 2.3 37.1 1.0
OD2 B:ASP252 2.4 32.5 1.0
O B:HOH766 2.6 35.6 1.0
CG B:ASP252 3.3 35.0 1.0
CG B:ASP145 3.3 31.6 1.0
CD B:GLU220 3.4 31.6 1.0
CD B:GLU218 3.4 40.2 1.0
CB B:ASP252 3.5 29.0 1.0
NZ B:LYS272 3.6 31.2 1.0
O B:HOH790 3.7 37.9 1.0
OD1 B:ASP145 3.8 30.8 1.0
OE2 B:GLU220 3.9 29.4 1.0
OH B:TYR178 3.9 33.3 1.0
CB B:GLU218 4.1 28.5 1.0
OE1 B:GLU218 4.3 39.0 1.0
CG B:GLU218 4.3 39.8 1.0
CE B:LYS272 4.5 31.9 1.0
OD1 B:ASP252 4.5 31.0 1.0
OG1 B:THR369 4.5 36.2 1.0
CG B:GLU220 4.6 37.2 1.0
CB B:ASP145 4.6 25.7 1.0
O B:PHE146 4.6 31.7 1.0
CA B:GLY368 4.6 31.3 1.0
N B:THR369 4.6 30.8 1.0
CE1 B:TYR178 4.9 32.6 1.0
CZ B:TYR178 4.9 35.6 1.0
O B:ASP252 5.0 28.6 1.0

Magnesium binding site 3 out of 8 in 5ti1

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Magnesium binding site 3 out of 8 in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:32.2
occ:1.00
 OE1 C:GLU220 2.2 34.2 1.0
OD2 C:ASP145 2.3 30.8 1.0
OE2 C:GLU218 2.3 36.2 1.0
O C:HOH753 2.4 31.3 1.0
OD2 C:ASP252 2.5 33.4 1.0
CG C:ASP145 3.3 31.4 1.0
CG C:ASP252 3.4 33.9 1.0
CD C:GLU220 3.4 35.1 1.0
CB C:ASP252 3.5 30.1 1.0
CD C:GLU218 3.5 38.1 1.0
O C:HOH756 3.7 39.3 1.0
OD1 C:ASP145 3.8 31.0 1.0
OH C:TYR178 3.8 37.6 1.0
NZ C:LYS272 3.9 34.7 1.0
OE2 C:GLU220 3.9 33.2 1.0
O C:HOH791 3.9 40.0 1.0
CB C:GLU218 4.2 42.0 1.0
OE1 C:GLU218 4.4 39.3 1.0
CG C:GLU218 4.4 41.1 1.0
OD1 C:ASP252 4.5 30.2 1.0
CA C:GLY368 4.6 26.9 1.0
CG C:GLU220 4.6 27.3 1.0
CE C:LYS272 4.6 36.4 1.0
OG1 C:THR369 4.6 34.9 1.0
CB C:ASP145 4.6 27.9 1.0
N C:THR369 4.7 33.4 1.0
O C:PHE146 4.7 25.5 1.0
CZ C:TYR178 4.8 33.4 1.0
CE1 C:TYR178 4.9 29.6 1.0
CA C:ASP252 4.9 24.7 1.0
O C:ASP252 5.0 28.2 1.0

Magnesium binding site 4 out of 8 in 5ti1

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Magnesium binding site 4 out of 8 in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:34.7
occ:1.00
 OE1 D:GLU218 2.1 36.5 1.0
OE2 D:GLU220 2.1 35.8 1.0
OD2 D:ASP145 2.3 26.9 1.0
OD2 D:ASP252 2.4 36.5 1.0
O D:HOH762 3.0 31.1 1.0
CG D:ASP252 3.2 34.2 1.0
CD D:GLU220 3.3 36.1 1.0
CG D:ASP145 3.3 25.5 1.0
CD D:GLU218 3.3 31.2 1.0
CB D:ASP252 3.4 29.2 1.0
NZ D:LYS272 3.6 30.9 1.0
OD1 D:ASP145 3.7 29.9 1.0
OH D:TYR178 3.8 29.5 1.0
OE1 D:GLU220 3.9 29.6 1.0
CB D:GLU218 4.0 23.4 1.0
O D:HOH670 4.1 35.6 1.0
OE2 D:GLU218 4.2 30.7 1.0
CG D:GLU218 4.2 26.0 1.0
OD1 D:ASP252 4.4 36.9 1.0
O D:HOH861 4.4 37.1 1.0
CG D:GLU220 4.5 20.4 1.0
OG1 D:THR369 4.5 32.4 1.0
CB D:ASP145 4.6 19.5 1.0
CE D:LYS272 4.7 31.4 1.0
CA D:GLY368 4.8 26.1 1.0
N D:THR369 4.8 25.3 1.0
O D:ASP252 4.8 27.5 1.0
CA D:ASP252 4.8 28.8 1.0
CZ D:TYR178 4.9 34.6 1.0
O D:PHE146 4.9 25.0 1.0
OH D:TYR143 4.9 23.9 1.0
O D:HOH751 5.0 20.9 1.0

Magnesium binding site 5 out of 8 in 5ti1

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Magnesium binding site 5 out of 8 in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:23.7
occ:1.00
 OE1 E:GLU220 2.2 24.7 1.0
OD2 E:ASP145 2.2 19.8 1.0
OE2 E:GLU218 2.3 26.5 1.0
OD2 E:ASP252 2.4 23.4 1.0
O E:HOH750 2.6 27.4 1.0
CG E:ASP252 3.3 23.6 1.0
CD E:GLU220 3.3 26.0 1.0
CG E:ASP145 3.3 23.6 1.0
O E:HOH701 3.4 36.1 1.0
CD E:GLU218 3.5 26.8 1.0
NZ E:LYS272 3.5 34.3 1.0
CB E:ASP252 3.5 21.1 1.0
OD1 E:ASP145 3.7 22.6 1.0
OE2 E:GLU220 3.8 19.1 1.0
O E:HOH703 3.9 36.9 1.0
OH E:TYR178 3.9 28.6 1.0
CB E:GLU218 4.1 16.2 1.0
CG E:GLU218 4.3 23.4 1.0
OE1 E:GLU218 4.4 29.3 1.0
OD1 E:ASP252 4.5 26.9 1.0
CG E:GLU220 4.5 14.8 1.0
OG1 E:THR369 4.5 20.8 1.0
O E:PHE146 4.6 23.8 1.0
N E:THR369 4.6 21.7 1.0
CA E:GLY368 4.6 16.4 1.0
CB E:ASP145 4.6 17.8 1.0
CE E:LYS272 4.7 32.2 1.0
O E:ASP252 4.9 18.2 1.0
CZ E:TYR178 4.9 27.2 1.0
CA E:ASP252 5.0 17.7 1.0
C E:GLY368 5.0 22.2 1.0
CE1 E:TYR178 5.0 27.1 1.0

Magnesium binding site 6 out of 8 in 5ti1

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Magnesium binding site 6 out of 8 in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:21.7
occ:1.00
 OE1 F:GLU220 2.2 20.1 1.0
OD2 F:ASP145 2.2 19.6 1.0
OE2 F:GLU218 2.2 25.3 1.0
OD2 F:ASP252 2.4 22.9 1.0
O F:HOH797 2.5 27.4 1.0
CG F:ASP145 3.3 20.2 1.0
CG F:ASP252 3.3 24.7 1.0
CD F:GLU220 3.3 24.1 1.0
NZ F:LYS272 3.4 23.6 1.0
CD F:GLU218 3.5 25.9 1.0
CB F:ASP252 3.5 16.3 1.0
OD1 F:ASP145 3.7 18.3 1.0
OE2 F:GLU220 3.8 20.5 1.0
OH F:TYR178 3.9 23.5 1.0
O F:HOH860 3.9 38.2 1.0
O F:HOH724 4.0 30.9 1.0
CB F:GLU218 4.2 22.7 1.0
OE1 F:GLU218 4.3 27.4 1.0
CG F:GLU218 4.4 25.1 1.0
OD1 F:ASP252 4.5 25.0 1.0
CE F:LYS272 4.5 31.4 1.0
CG F:GLU220 4.6 17.4 1.0
CB F:ASP145 4.6 15.6 1.0
O F:PHE146 4.6 18.4 1.0
CA F:GLY368 4.6 15.2 1.0
OG1 F:THR369 4.7 24.7 1.0
N F:THR369 4.7 18.1 1.0
CZ F:TYR178 4.9 26.9 1.0
CE1 F:TYR178 4.9 24.1 1.0
O F:ASP252 5.0 18.2 1.0
CA F:ASP252 5.0 18.3 1.0
O F:HOH630 5.0 15.3 1.0

Magnesium binding site 7 out of 8 in 5ti1

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Magnesium binding site 7 out of 8 in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:21.0
occ:1.00
 OE2 G:GLU218 2.2 23.4 1.0
OD2 G:ASP145 2.2 18.4 1.0
OE1 G:GLU220 2.3 20.5 1.0
OD2 G:ASP252 2.4 27.2 1.0
O G:HOH792 2.4 21.0 1.0
CG G:ASP252 3.3 26.5 1.0
CG G:ASP145 3.3 23.0 1.0
CD G:GLU220 3.4 24.5 1.0
CD G:GLU218 3.4 26.4 1.0
CB G:ASP252 3.5 18.2 1.0
NZ G:LYS272 3.5 25.8 1.0
O G:HOH739 3.7 26.2 1.0
OH G:TYR178 3.8 22.6 1.0
OD1 G:ASP145 3.8 19.2 1.0
OE2 G:GLU220 3.9 21.7 1.0
O G:HOH893 4.0 33.3 1.0
CB G:GLU218 4.1 22.9 1.0
CG G:GLU218 4.3 25.3 1.0
OE1 G:GLU218 4.3 25.2 1.0
CE G:LYS272 4.5 32.8 1.0
OD1 G:ASP252 4.5 22.9 1.0
OG1 G:THR369 4.5 27.2 1.0
CA G:GLY368 4.6 15.1 1.0
O G:PHE146 4.6 21.0 1.0
CB G:ASP145 4.6 12.8 1.0
CG G:GLU220 4.6 18.7 1.0
N G:THR369 4.7 20.5 1.0
CZ G:TYR178 4.8 25.6 1.0
CE1 G:TYR178 4.8 21.9 1.0
C G:GLY368 5.0 18.7 1.0
CA G:ASP252 5.0 15.9 1.0
O G:ASP252 5.0 18.9 1.0

Magnesium binding site 8 out of 8 in 5ti1

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Magnesium binding site 8 out of 8 in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:22.2
occ:1.00
 OE1 H:GLU220 2.1 19.4 1.0
OE2 H:GLU218 2.2 24.3 1.0
OD2 H:ASP145 2.3 26.2 1.0
OD2 H:ASP252 2.5 26.0 1.0
O H:HOH775 2.6 28.7 1.0
CD H:GLU220 3.3 17.8 1.0
CG H:ASP252 3.4 25.3 1.0
CG H:ASP145 3.4 22.4 1.0
CD H:GLU218 3.4 24.7 1.0
CB H:ASP252 3.5 15.7 1.0
NZ H:LYS272 3.6 19.7 1.0
O H:HOH702 3.7 24.0 1.0
OD1 H:ASP145 3.8 24.0 1.0
OE2 H:GLU220 3.8 16.2 1.0
O H:HOH889 3.8 37.5 1.0
OH H:TYR178 4.0 25.6 1.0
CB H:GLU218 4.0 14.5 1.0
CG H:GLU218 4.2 20.5 1.0
OE1 H:GLU218 4.3 28.7 1.0
OG1 H:THR369 4.5 24.9 1.0
CG H:GLU220 4.5 14.4 1.0
CE H:LYS272 4.5 28.3 1.0
OD1 H:ASP252 4.6 26.1 1.0
N H:THR369 4.6 15.4 1.0
CA H:GLY368 4.6 13.1 1.0
O H:PHE146 4.6 16.6 1.0
CB H:ASP145 4.7 15.0 1.0
O H:ASP252 4.9 19.3 1.0
C H:GLY368 4.9 16.7 1.0
CA H:ASP252 5.0 10.9 1.0
CZ H:TYR178 5.0 26.7 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease, S.L.Delker, J.Abendroth, D.Lorimer, T.E.Edwards. Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400 To Be Published.
Page generated: Mon Dec 14 21:12:12 2020

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