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Sodium in PDB 5dlv: Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)

Enzymatic activity of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)

All present enzymatic activity of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca):
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca), PDB code: 5dlv was solved by W.J.Keune, T.Heidebrecht, E.Von Castelmur, R.P.Joosten, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.61 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 62.880, 77.832, 92.437, 83.84, 79.29, 77.08
R / Rfree (%) 19.3 / 22.7

Other elements in 5dlv:

The structure of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Iodine (I) 27 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) (pdb code 5dlv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca), PDB code: 5dlv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5dlv

Go back to Sodium Binding Sites List in 5dlv
Sodium binding site 1 out of 4 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


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 Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na928

b:37.8
occ:1.00
 O A:MET675 2.4 40.7 1.0
O A:HOH1252 2.4 43.3 1.0
O A:HOH1246 2.5 38.6 1.0
O A:ASP672 2.5 38.9 1.0
O A:HOH1274 2.5 57.7 1.0
O A:TYR669 2.6 41.9 1.0
C A:MET675 3.4 40.6 1.0
C A:ASP672 3.7 41.9 1.0
C A:TYR669 3.8 42.4 1.0
N A:SER676 4.2 37.8 1.0
N A:MET675 4.2 40.7 1.0
CA A:SER676 4.3 36.5 1.0
CA A:LYS673 4.4 46.2 1.0
CA A:MET675 4.4 39.6 1.0
C A:LYS673 4.5 46.9 1.0
N A:LYS673 4.5 44.4 1.0
CA A:TYR669 4.6 40.7 1.0
O A:LYS673 4.6 47.1 1.0
O A:LYS670 4.6 44.4 1.0
N A:LYS670 4.7 44.0 1.0
CA A:ASP672 4.7 42.8 1.0
CA A:LYS670 4.8 47.4 1.0
C A:LYS670 4.9 45.5 1.0
N A:ASP672 4.9 45.0 1.0
CB A:SER676 4.9 37.2 1.0
N A:GLN674 4.9 47.6 1.0
CB A:TYR669 4.9 40.5 1.0
C A:GLN674 4.9 44.8 1.0
CB A:ASP672 5.0 42.3 1.0

Sodium binding site 2 out of 4 in 5dlv

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Sodium binding site 2 out of 4 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


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 Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na929

b:39.0
occ:1.00
 O A:HOH1175 2.4 41.0 1.0
O A:HOH1224 2.4 24.6 1.0
O A:HOH1273 2.4 44.6 1.0
OG A:SER807 2.4 33.4 1.0
O A:ASN801 2.5 25.8 1.0
O A:SER804 2.6 31.5 1.0
C A:ASN801 3.4 26.6 1.0
CB A:SER807 3.6 34.0 1.0
C A:SER804 3.6 31.9 1.0
CA A:ASP802 3.8 28.6 1.0
N A:ASP802 3.9 27.4 1.0
O A:ASP802 4.2 27.2 1.0
N A:SER807 4.2 33.0 1.0
C A:ASP802 4.2 28.0 1.0
CA A:CYS805 4.3 32.2 1.0
N A:CYS805 4.4 31.5 1.0
O A:HOH1008 4.4 35.0 1.0
CA A:SER807 4.4 34.4 1.0
CB A:ASN801 4.4 26.4 1.0
N A:SER804 4.5 29.6 1.0
CA A:ASN801 4.5 26.1 1.0
C A:CYS805 4.5 32.7 1.0
O A:HOH1180 4.5 35.2 1.0
CA A:SER804 4.5 30.3 1.0
OD1 A:ASP802 4.6 31.8 1.0
O A:CYS805 4.6 32.1 1.0
CB A:SER804 4.9 31.9 1.0

Sodium binding site 3 out of 4 in 5dlv

Go back to Sodium Binding Sites List in 5dlv
Sodium binding site 3 out of 4 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


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 Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na925

b:39.9
occ:1.00
 O B:MET675 2.4 38.6 1.0
O B:HOH1250 2.4 42.2 1.0
O B:HOH1192 2.6 39.9 1.0
O B:ASP672 2.6 39.2 1.0
O B:HOH1276 2.8 44.0 1.0
O B:TYR669 2.8 41.0 1.0
C B:MET675 3.4 38.8 1.0
C B:ASP672 3.8 42.3 1.0
C B:TYR669 4.0 42.4 1.0
N B:SER676 4.1 37.2 1.0
N B:MET675 4.1 39.5 1.0
CA B:SER676 4.2 36.5 1.0
CA B:LYS673 4.3 47.1 1.0
CA B:MET675 4.3 38.4 1.0
C B:LYS673 4.4 46.4 1.0
O B:LYS673 4.5 47.4 1.0
N B:LYS673 4.5 44.8 1.0
O B:LYS670 4.8 45.7 1.0
CB B:SER676 4.8 36.6 1.0
CA B:TYR669 4.8 40.3 1.0
N B:GLN674 4.8 46.2 1.0
C B:GLN674 4.8 41.6 1.0
CA B:ASP672 4.9 42.6 1.0
N B:LYS670 4.9 46.0 1.0

Sodium binding site 4 out of 4 in 5dlv

Go back to Sodium Binding Sites List in 5dlv
Sodium binding site 4 out of 4 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca)


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 Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na926

b:44.4
occ:1.00
 O B:HOH1253 2.3 42.3 1.0
O B:HOH1160 2.3 43.7 1.0
O B:HOH1183 2.4 22.6 1.0
O B:SER804 2.5 31.6 1.0
OG B:SER807 2.6 34.5 1.0
O B:ASN801 2.7 28.1 1.0
C B:SER804 3.6 31.6 1.0
C B:ASN801 3.6 27.8 1.0
CB B:SER807 3.7 34.2 1.0
CA B:ASP802 3.9 28.0 1.0
N B:ASP802 4.1 27.9 1.0
CA B:CYS805 4.1 32.9 1.0
N B:SER807 4.2 35.4 1.0
O B:ASP802 4.2 26.1 1.0
N B:CYS805 4.3 31.4 1.0
C B:ASP802 4.3 27.4 1.0
C B:CYS805 4.3 33.4 1.0
O B:HOH1077 4.4 41.4 1.0
O B:CYS805 4.4 33.1 1.0
O B:HOH1082 4.4 43.3 1.0
CA B:SER807 4.5 35.8 1.0
N B:SER804 4.5 29.7 1.0
CA B:SER804 4.6 30.0 1.0
CB B:ASN801 4.7 28.6 1.0
OD1 B:ASP802 4.7 30.1 1.0
CA B:ASN801 4.7 27.7 1.0
N B:ALA806 4.9 33.1 1.0
CB B:SER804 5.0 30.8 1.0

Reference:

W.J.Keune, J.Hausmann, R.Bolier, D.Tolenaars, A.Kremer, T.Heidebrecht, R.P.Joosten, M.Sunkara, A.J.Morris, E.Matas-Rico, W.H.Moolenaar, R.P.Oude Elferink, A.Perrakis. Steroid Binding to Autotaxin Links Bile Salts and Lysophosphatidic Acid Signalling. Nat Commun V. 7 11248 2016.
ISSN: ESSN 2041-1723
PubMed: 27075612
DOI: 10.1038/NCOMMS11248
Page generated: Mon Oct 7 20:38:27 2024

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