Atomistry » Zinc » PDB 5dag-5drq » 5dlw
Atomistry »
  Zinc »
    PDB 5dag-5drq »
      5dlw »

Zinc in PDB 5dlw: Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)

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

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

Protein crystallography data

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

Resolution Low / High (Å) 79.03 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.197, 93.051, 149.680, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.6

Other elements in 5dlw:

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

Iodine (I) 13 atoms
Calcium (Ca) 1 atom
Sodium (Na) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 5dlw

Go back to Zinc Binding Sites List in 5dlw
Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:79.9
occ:1.00
 OG1 A:THR209 1.7 42.3 1.0
OD1 A:ASP171 2.0 39.5 1.0
NE2 A:HIS359 2.2 19.9 1.0
OAD A:NKP904 2.5 40.4 1.0
OD2 A:ASP358 2.6 39.6 1.0
CG A:ASP171 2.8 37.6 1.0
CB A:THR209 2.8 29.6 1.0
OD2 A:ASP171 3.0 48.1 1.0
CE1 A:HIS359 3.1 20.5 1.0
CD2 A:HIS359 3.2 20.1 1.0
CA A:THR209 3.3 22.8 1.0
CG2 A:THR209 3.3 29.7 1.0
CG A:ASP358 3.4 29.1 1.0
OAB A:NKP904 3.5 31.1 1.0
PAC A:NKP904 3.5 39.0 1.0
N A:THR209 3.6 21.1 1.0
OD1 A:ASP358 3.6 30.6 1.0
OAF A:NKP904 4.0 41.2 1.0
CB A:ASP171 4.1 32.2 1.0
ND1 A:HIS359 4.2 20.2 1.0
OD1 A:ASP311 4.2 24.6 1.0
CG A:HIS359 4.2 19.5 1.0
CAG A:NKP904 4.2 46.4 1.0
CE1 A:HIS474 4.4 22.4 1.0
N A:GLY172 4.4 25.1 1.0
CG A:ASP311 4.4 26.7 1.0
CA A:ASP171 4.5 25.9 1.0
C A:LYS208 4.5 20.5 1.0
ZN A:ZN902 4.5 26.4 1.0
NE2 A:HIS474 4.6 24.2 1.0
CB A:ASP358 4.6 27.1 1.0
C A:THR209 4.7 21.8 1.0
OD2 A:ASP311 4.7 25.8 1.0
C A:ASP171 4.8 24.5 1.0
OAA A:NKP904 4.8 31.9 1.0
CB A:ASP311 5.0 25.5 1.0
OH A:TYR306 5.0 31.9 0.5

Zinc binding site 2 out of 2 in 5dlw

Go back to Zinc Binding Sites List in 5dlw
Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Autotaxin (ENPP2) with Tauroursodeoxycholic Acid (Tudca) and Lysophosphatidic Acid (Lpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:26.4
occ:1.00
 NE2 A:HIS315 2.1 23.9 1.0
NE2 A:HIS474 2.2 24.2 1.0
OD1 A:ASP311 2.3 24.6 1.0
OAD A:NKP904 2.4 40.4 1.0
OD2 A:ASP311 2.5 25.8 1.0
OAA A:NKP904 2.5 31.9 1.0
CG A:ASP311 2.7 26.7 1.0
PAC A:NKP904 2.9 39.0 1.0
CE1 A:HIS315 3.0 26.4 1.0
CD2 A:HIS315 3.1 25.5 1.0
CD2 A:HIS474 3.1 22.3 1.0
CE1 A:HIS474 3.2 22.4 1.0
OAB A:NKP904 3.9 31.1 1.0
ND1 A:HIS315 4.1 28.5 1.0
CE1 A:HIS359 4.2 20.5 1.0
CG A:HIS315 4.2 25.4 1.0
OAF A:NKP904 4.2 41.2 1.0
CB A:ASP311 4.2 25.5 1.0
CG A:HIS474 4.3 22.3 1.0
ND1 A:HIS474 4.3 23.2 1.0
CE A:MET361 4.5 22.8 1.0
CAG A:NKP904 4.5 46.4 1.0
ZN A:ZN901 4.5 79.9 1.0
NE2 A:HIS359 4.5 19.9 1.0
OD1 A:ASP171 4.6 39.5 1.0
OG1 A:THR209 4.9 42.3 1.0
O A:ASP311 4.9 23.7 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: Sun Oct 27 14:50:03 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy