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Sodium 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:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Fumarylacetoacetate Hydrolase From Burkholderia Xenovorans LB400, PDB code: 5ti1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5ti1

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Sodium 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 Sodium with other atoms in the Na 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:Na502

b:23.7
occ:0.90
 OD1 A:ASP252 2.4 39.9 1.0
O A:LYS272 2.4 23.4 1.0
O A:ALA275 2.5 17.5 1.0
O A:TRP253 2.5 23.5 1.0
OG1 A:THR276 3.1 23.2 1.0
N A:TRP253 3.2 21.9 1.0
C A:LYS272 3.4 25.9 1.0
C A:ASP252 3.4 22.7 1.0
C A:TRP253 3.4 28.6 1.0
CG A:ASP252 3.5 33.2 1.0
C A:ALA275 3.6 18.1 1.0
CA A:LYS272 3.7 27.4 1.0
CA A:ASP252 3.7 24.7 1.0
CA A:TRP253 3.8 25.2 1.0
O A:ASP252 4.0 21.9 1.0
CB A:LYS272 4.1 27.1 1.0
CB A:THR276 4.2 20.5 1.0
CB A:TRP253 4.2 19.4 1.0
O A:HOH659 4.2 32.5 1.0
CA A:THR276 4.2 18.6 1.0
CB A:ASP252 4.2 25.9 1.0
N A:THR276 4.3 16.3 1.0
OD2 A:ASP252 4.4 32.3 1.0
N A:ALA275 4.5 23.2 1.0
CD A:LYS272 4.6 39.7 1.0
N A:THR273 4.6 22.3 1.0
CA A:ALA275 4.7 18.0 1.0
N A:SER254 4.7 25.5 1.0
O A:HOH685 4.8 18.4 1.0
CG2 A:THR276 4.8 22.8 1.0
O A:HOH779 4.8 21.1 1.0
CG A:LYS272 5.0 36.3 1.0
CD1 A:TRP253 5.0 19.6 1.0

Sodium binding site 2 out of 8 in 5ti1

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Sodium 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 Sodium with other atoms in the Na 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:Na502

b:22.5
occ:0.78
 OD1 B:ASP252 2.4 31.0 1.0
O B:ALA275 2.4 25.1 1.0
O B:LYS272 2.4 23.4 1.0
O B:TRP253 2.5 31.8 1.0
OG1 B:THR276 2.9 26.4 1.0
N B:TRP253 3.2 27.3 1.0
C B:ASP252 3.4 26.9 1.0
C B:LYS272 3.5 27.6 1.0
C B:TRP253 3.5 29.3 1.0
C B:ALA275 3.5 22.9 1.0
CG B:ASP252 3.5 35.0 1.0
CA B:ASP252 3.7 24.7 1.0
CA B:TRP253 3.7 24.7 1.0
CA B:LYS272 3.9 22.8 1.0
CB B:THR276 4.0 23.3 1.0
O B:ASP252 4.0 28.6 1.0
CA B:THR276 4.1 21.8 1.0
CB B:TRP253 4.1 29.0 1.0
N B:THR276 4.1 23.5 1.0
O B:HOH671 4.2 27.4 1.0
CB B:ASP252 4.2 29.0 1.0
CB B:LYS272 4.3 22.9 1.0
N B:ALA275 4.5 20.7 1.0
OD2 B:ASP252 4.5 32.5 1.0
CA B:ALA275 4.6 20.8 1.0
N B:THR273 4.6 21.8 1.0
CG2 B:THR276 4.7 24.9 1.0
N B:SER254 4.7 32.8 1.0
O B:HOH705 4.7 16.4 1.0
CD B:LYS272 4.8 31.2 1.0
CD1 B:TRP253 4.9 24.6 1.0
O B:ASN251 4.9 26.3 1.0
CG B:TRP253 4.9 29.4 1.0
O B:HOH703 4.9 22.3 1.0

Sodium binding site 3 out of 8 in 5ti1

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Sodium 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 Sodium with other atoms in the Na 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:Na502

b:20.8
occ:0.82
 O C:ALA275 2.3 27.2 1.0
OD1 C:ASP252 2.3 30.2 1.0
O C:LYS272 2.4 27.4 1.0
O C:TRP253 2.4 24.6 1.0
OG1 C:THR276 3.1 26.6 1.0
N C:TRP253 3.2 27.9 1.0
C C:LYS272 3.4 28.8 1.0
C C:ALA275 3.4 24.8 1.0
C C:ASP252 3.4 26.2 1.0
C C:TRP253 3.4 31.3 1.0
CG C:ASP252 3.5 33.9 1.0
CA C:LYS272 3.7 28.3 1.0
CA C:TRP253 3.7 32.7 1.0
CA C:ASP252 3.7 24.7 1.0
O C:ASP252 4.0 28.2 1.0
O C:HOH639 4.0 27.1 1.0
CB C:LYS272 4.1 25.7 1.0
N C:THR276 4.1 26.5 1.0
CB C:TRP253 4.1 28.6 1.0
CA C:THR276 4.1 22.5 1.0
CB C:THR276 4.1 22.4 1.0
CB C:ASP252 4.2 30.1 1.0
N C:ALA275 4.4 24.2 1.0
OD2 C:ASP252 4.4 33.4 1.0
CA C:ALA275 4.5 24.5 1.0
N C:THR273 4.6 26.1 1.0
N C:SER254 4.6 29.3 1.0
CD C:LYS272 4.7 39.2 1.0
CG2 C:THR276 4.8 23.2 1.0
O C:HOH774 4.9 28.3 1.0
O C:HOH668 4.9 23.0 1.0
CD1 C:TRP253 4.9 24.7 1.0
CG C:TRP253 5.0 32.4 1.0
O C:ASN251 5.0 29.2 1.0
N C:LYS272 5.0 22.7 1.0

Sodium binding site 4 out of 8 in 5ti1

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Sodium 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 Sodium with other atoms in the Na 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:Na502

b:20.2
occ:0.92
 OD1 D:ASP252 2.3 36.9 1.0
O D:TRP253 2.3 21.5 1.0
O D:ALA275 2.4 28.0 1.0
O D:LYS272 2.4 23.5 1.0
N D:TRP253 3.0 25.4 1.0
OG1 D:THR276 3.0 20.2 1.0
C D:ASP252 3.2 26.8 1.0
C D:TRP253 3.3 22.8 1.0
CG D:ASP252 3.4 34.2 1.0
C D:LYS272 3.4 19.9 1.0
C D:ALA275 3.5 17.8 1.0
CA D:TRP253 3.6 24.6 1.0
CA D:ASP252 3.6 28.8 1.0
CA D:LYS272 3.7 27.8 1.0
O D:ASP252 3.7 27.5 1.0
CB D:TRP253 4.0 24.5 1.0
CB D:ASP252 4.1 29.2 1.0
CB D:THR276 4.1 17.4 1.0
CA D:THR276 4.1 17.7 1.0
CB D:LYS272 4.1 34.1 1.0
N D:THR276 4.2 18.3 1.0
O D:HOH751 4.3 20.9 1.0
OD2 D:ASP252 4.3 36.5 1.0
N D:SER254 4.5 24.4 1.0
N D:ALA275 4.5 23.1 1.0
CA D:ALA275 4.6 18.4 1.0
N D:THR273 4.7 23.5 1.0
O D:HOH695 4.8 22.3 1.0
CD1 D:TRP253 4.8 20.7 1.0
CG2 D:THR276 4.8 19.2 1.0
CG D:TRP253 4.8 23.6 1.0
OG D:SER254 4.9 33.9 1.0
O D:ASN251 4.9 28.1 1.0
N D:ASP252 4.9 32.0 1.0
O D:HOH839 4.9 17.8 1.0
CD D:LYS272 5.0 36.5 1.0

Sodium binding site 5 out of 8 in 5ti1

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Sodium 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 Sodium with other atoms in the Na 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:Na502

b:21.9
occ:0.88
 O E:ALA275 2.4 14.6 1.0
OD1 E:ASP252 2.4 26.9 1.0
O E:LYS272 2.5 19.8 1.0
O E:TRP253 2.6 19.8 1.0
OG1 E:THR276 2.9 16.5 1.0
N E:TRP253 3.2 19.1 1.0
C E:ASP252 3.4 19.2 1.0
C E:ALA275 3.5 12.8 1.0
C E:LYS272 3.5 19.4 1.0
C E:TRP253 3.6 19.2 1.0
CG E:ASP252 3.6 23.6 1.0
CA E:ASP252 3.7 17.7 1.0
CA E:TRP253 3.8 19.6 1.0
CA E:LYS272 3.9 17.3 1.0
O E:HOH667 4.0 18.4 1.0
CB E:THR276 4.0 15.0 1.0
O E:ASP252 4.0 18.2 1.0
CA E:THR276 4.0 12.3 1.0
N E:THR276 4.1 13.0 1.0
CB E:TRP253 4.2 17.6 1.0
CB E:LYS272 4.2 20.4 1.0
CB E:ASP252 4.3 21.1 1.0
OD2 E:ASP252 4.5 23.4 1.0
CD E:LYS272 4.5 32.9 1.0
O E:HOH627 4.6 14.9 1.0
N E:ALA275 4.6 21.3 1.0
CG2 E:THR276 4.7 16.2 1.0
CA E:ALA275 4.7 20.8 1.0
O E:HOH815 4.7 14.2 1.0
N E:THR273 4.7 15.7 1.0
N E:SER254 4.8 16.4 1.0
O E:ASN251 4.9 18.1 1.0
CD1 E:TRP253 4.9 13.9 1.0
CG E:TRP253 5.0 18.9 1.0

Sodium binding site 6 out of 8 in 5ti1

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Sodium 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 Sodium with other atoms in the Na 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:Na502

b:18.8
occ:0.92
 O F:ALA275 2.4 15.8 1.0
OD1 F:ASP252 2.4 25.0 1.0
O F:LYS272 2.4 15.9 1.0
O F:TRP253 2.5 17.6 1.0
OG1 F:THR276 3.0 18.1 1.0
N F:TRP253 3.3 13.1 1.0
C F:LYS272 3.4 20.7 1.0
C F:ASP252 3.4 20.2 1.0
C F:ALA275 3.4 16.5 1.0
C F:TRP253 3.5 16.5 1.0
CG F:ASP252 3.5 24.7 1.0
CA F:LYS272 3.8 16.5 1.0
CA F:ASP252 3.8 18.3 1.0
CA F:TRP253 3.8 19.2 1.0
O F:ASP252 4.0 18.2 1.0
O F:HOH630 4.0 15.3 1.0
CB F:TRP253 4.1 17.2 1.0
CA F:THR276 4.1 15.9 1.0
N F:THR276 4.1 16.3 1.0
CB F:THR276 4.1 18.5 1.0
CB F:LYS272 4.2 16.8 1.0
CB F:ASP252 4.2 16.3 1.0
N F:ALA275 4.4 15.4 1.0
OD2 F:ASP252 4.4 22.9 1.0
CD F:LYS272 4.6 32.3 1.0
CA F:ALA275 4.6 15.6 1.0
N F:THR273 4.6 14.4 1.0
N F:SER254 4.7 17.9 1.0
O F:HOH705 4.8 13.6 1.0
O F:HOH808 4.9 17.2 1.0
CD1 F:TRP253 4.9 12.3 1.0
CG2 F:THR276 4.9 14.0 1.0
CG F:TRP253 4.9 12.8 1.0

Sodium binding site 7 out of 8 in 5ti1

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Sodium 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 Sodium with other atoms in the Na 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:Na502

b:18.8
occ:0.91
 OD1 G:ASP252 2.3 22.9 1.0
O G:ALA275 2.4 18.0 1.0
O G:LYS272 2.4 16.3 1.0
O G:TRP253 2.4 25.5 1.0
OG1 G:THR276 3.1 21.7 1.0
N G:TRP253 3.2 14.3 1.0
C G:ASP252 3.4 14.2 1.0
C G:LYS272 3.4 17.0 1.0
C G:TRP253 3.4 24.9 1.0
C G:ALA275 3.5 14.5 1.0
CG G:ASP252 3.5 26.5 1.0
CA G:LYS272 3.7 17.1 1.0
CA G:ASP252 3.7 15.9 1.0
CA G:TRP253 3.7 24.1 1.0
O G:ASP252 4.0 18.9 1.0
CB G:LYS272 4.1 20.1 1.0
CB G:TRP253 4.1 16.2 1.0
CA G:THR276 4.1 15.9 1.0
CB G:THR276 4.1 22.8 1.0
N G:THR276 4.2 14.4 1.0
O G:HOH794 4.2 19.8 1.0
CB G:ASP252 4.2 18.2 1.0
N G:ALA275 4.5 19.5 1.0
OD2 G:ASP252 4.5 27.2 1.0
CA G:ALA275 4.6 16.9 1.0
N G:THR273 4.6 12.1 1.0
N G:SER254 4.6 20.6 1.0
CD G:LYS272 4.7 37.2 1.0
O G:HOH681 4.8 16.1 1.0
CG2 G:THR276 4.9 12.9 1.0
O G:ASN251 4.9 15.9 1.0
CD1 G:TRP253 4.9 19.2 1.0
O G:HOH773 4.9 12.9 1.0
CG G:TRP253 5.0 20.3 1.0

Sodium binding site 8 out of 8 in 5ti1

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Sodium 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 Sodium with other atoms in the Na 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:Na502

b:17.5
occ:0.77
 OD1 H:ASP252 2.4 26.1 1.0
O H:ALA275 2.4 15.4 1.0
O H:LYS272 2.5 17.2 1.0
O H:TRP253 2.5 16.6 1.0
OG1 H:THR276 3.0 24.3 1.0
N H:TRP253 3.1 20.1 1.0
C H:ASP252 3.4 17.7 1.0
C H:ALA275 3.5 13.3 1.0
C H:TRP253 3.5 23.0 1.0
C H:LYS272 3.5 18.1 1.0
CG H:ASP252 3.5 25.3 1.0
CA H:ASP252 3.7 10.9 1.0
CA H:TRP253 3.7 20.8 1.0
CA H:LYS272 3.8 17.2 1.0
O H:ASP252 4.0 19.3 1.0
CB H:THR276 4.0 17.8 1.0
CA H:THR276 4.1 15.4 1.0
N H:THR276 4.1 13.4 1.0
CB H:TRP253 4.1 15.8 1.0
O H:HOH756 4.2 21.4 1.0
CB H:ASP252 4.2 15.7 1.0
CB H:LYS272 4.3 18.0 1.0
OD2 H:ASP252 4.5 26.0 1.0
N H:ALA275 4.5 15.7 1.0
CA H:ALA275 4.6 13.5 1.0
CD H:LYS272 4.7 29.7 1.0
O H:HOH713 4.7 14.4 1.0
N H:THR273 4.7 13.7 1.0
CG2 H:THR276 4.7 13.8 1.0
N H:SER254 4.7 20.6 1.0
O H:HOH822 4.8 11.3 1.0
O H:ASN251 4.9 17.2 1.0
CD1 H:TRP253 4.9 12.4 1.0
CG H:TRP253 4.9 12.5 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: Tue Dec 15 11:37:30 2020

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