Zinc in PDB 5l0k: Crystal Structure of Autotaxin and Compound Pf-8380

All present enzymatic activity of Crystal Structure of Autotaxin and Compound Pf-8380:
3.1.4.39;

The structure of Crystal Structure of Autotaxin and Compound Pf-8380, PDB code: 5l0k was solved by J.D.Durbin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.23 / 2.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.924, 121.422, 156.247, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27

The structure of Crystal Structure of Autotaxin and Compound Pf-8380 also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Autotaxin and Compound Pf-8380 (pdb code 5l0k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Autotaxin and Compound Pf-8380, PDB code: 5l0k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Autotaxin and Compound Pf-8380


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 and Compound Pf-8380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:37.8 occ:1.00 NE2 A:HIS315 2.1 34.4 1.0 N31 A:6ZO906 2.1 51.7 1.0 NE2 A:HIS474 2.1 30.2 1.0 OD1 A:ASP311 2.2 33.7 1.0 OD2 A:ASP311 2.6 32.7 1.0 CG A:ASP311 2.7 34.3 1.0 CE1 A:HIS315 3.0 36.2 1.0 CD2 A:HIS474 3.1 31.1 1.0 C30 A:6ZO906 3.1 54.8 1.0 CD2 A:HIS315 3.1 35.6 1.0 CE1 A:HIS474 3.1 29.4 1.0 C28 A:6ZO906 3.2 54.4 1.0 O32 A:6ZO906 3.3 55.0 1.0 C27 A:6ZO906 3.7 54.4 1.0 ND1 A:HIS315 4.1 35.7 1.0 CB A:ASP311 4.2 34.2 1.0 OG1 A:THR209 4.2 36.1 1.0 CG A:HIS474 4.2 30.7 1.0 ND1 A:HIS474 4.2 29.3 1.0 CG A:HIS315 4.2 36.3 1.0 C26 A:6ZO906 4.3 55.1 1.0 CE1 A:HIS359 4.3 25.5 1.0 O29 A:6ZO906 4.3 54.2 1.0 ZN A:ZN904 4.4 54.4 1.0 NE2 A:HIS359 4.5 27.5 1.0 OD1 A:ASP171 4.6 36.8 1.0 O A:HOH1027 4.6 37.4 1.0 CE A:MET361 4.8 35.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Autotaxin and Compound Pf-8380


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 and Compound Pf-8380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:54.4 occ:1.00 OD1 A:ASP171 2.1 36.8 1.0 NE2 A:HIS359 2.1 27.5 1.0 OG1 A:THR209 2.3 36.1 1.0 OD2 A:ASP358 2.3 31.1 1.0 CG A:ASP171 2.8 35.2 1.0 OD2 A:ASP171 2.9 40.2 1.0 CB A:THR209 3.0 33.4 1.0 CE1 A:HIS359 3.0 25.5 1.0 CD2 A:HIS359 3.1 25.2 1.0 CA A:THR209 3.1 33.1 1.0 CG A:ASP358 3.2 31.5 1.0 CG2 A:THR209 3.2 30.9 1.0 OD1 A:ASP358 3.5 33.4 1.0 N A:THR209 3.6 32.9 1.0 C27 A:6ZO906 4.0 54.4 1.0 ND1 A:HIS359 4.1 26.4 1.0 CG A:HIS359 4.1 26.3 1.0 CB A:ASP171 4.2 33.4 1.0 CE1 A:HIS474 4.2 29.4 1.0 OD1 A:ASP311 4.3 33.7 1.0 N A:GLY172 4.3 30.4 1.0 NE2 A:HIS474 4.4 30.2 1.0 CB A:ASP358 4.4 29.2 1.0 C A:LYS208 4.4 32.5 1.0 ZN A:ZN903 4.4 37.8 1.0 C A:THR209 4.5 33.4 1.0 CG A:ASP311 4.5 34.3 1.0 CA A:ASP171 4.6 33.0 1.0 C28 A:6ZO906 4.6 54.4 1.0 N31 A:6ZO906 4.7 51.7 1.0 C A:ASP171 4.8 31.5 1.0 C25 A:6ZO906 4.8 54.9 1.0 O A:THR209 4.9 33.8 1.0 OD2 A:ASP311 4.9 32.7 1.0 O A:LYS208 5.0 32.2 1.0 CB A:ASP311 5.0 34.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Autotaxin and Compound Pf-8380


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Autotaxin and Compound Pf-8380 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:37.5 occ:1.00 NE2 B:HIS474 2.0 29.7 1.0 NE2 B:HIS315 2.1 39.2 1.0 N31 B:6ZO907 2.1 58.0 1.0 OD1 B:ASP311 2.3 36.2 1.0 OD2 B:ASP311 2.4 35.4 1.0 CG B:ASP311 2.7 38.3 1.0 CE1 B:HIS474 3.0 31.1 1.0 CE1 B:HIS315 3.1 41.1 1.0 CD2 B:HIS474 3.1 29.7 1.0 CD2 B:HIS315 3.1 41.7 1.0 C28 B:6ZO907 3.1 61.8 1.0 C30 B:6ZO907 3.2 61.2 1.0 O32 B:6ZO907 3.4 61.5 1.0 C27 B:6ZO907 3.5 61.0 1.0 ND1 B:HIS474 4.1 32.3 1.0 CB B:ASP311 4.2 37.4 1.0 CG B:HIS474 4.2 32.5 1.0 ND1 B:HIS315 4.2 41.2 1.0 CG B:HIS315 4.3 41.1 1.0 C26 B:6ZO907 4.3 62.7 1.0 OG1 B:THR209 4.3 38.9 1.0 CE1 B:HIS359 4.3 28.0 1.0 O29 B:6ZO907 4.4 63.4 1.0 OD2 B:ASP171 4.5 38.7 1.0 ZN B:ZN905 4.5 63.6 1.0 NE2 B:HIS359 4.5 26.2 1.0 CE B:MET361 4.7 39.3 1.0 C25 B:6ZO907 4.9 60.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Autotaxin and Compound Pf-8380


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Autotaxin and Compound Pf-8380 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn905 b:63.6 occ:1.00 OD2 B:ASP358 2.0 36.1 1.0 OD2 B:ASP171 2.1 38.7 1.0 NE2 B:HIS359 2.2 26.2 1.0 OG1 B:THR209 2.2 38.9 1.0 CG B:ASP171 2.8 36.1 1.0 OD1 B:ASP171 2.9 37.6 1.0 CB B:THR209 2.9 36.5 1.0 CE1 B:HIS359 3.0 28.0 1.0 CG B:ASP358 3.1 31.2 1.0 CD2 B:HIS359 3.1 26.9 1.0 CG2 B:THR209 3.1 36.7 1.0 CA B:THR209 3.2 36.2 1.0 OD1 B:ASP358 3.6 34.0 1.0 N B:THR209 3.8 36.2 1.0 C27 B:6ZO907 4.0 61.0 1.0 ND1 B:HIS359 4.1 27.8 1.0 CG B:HIS359 4.1 28.5 1.0 CB B:ASP171 4.2 35.1 1.0 N B:GLY172 4.3 33.7 1.0 CB B:ASP358 4.3 29.4 1.0 CE1 B:HIS474 4.4 31.1 1.0 OD1 B:ASP311 4.4 36.2 1.0 C B:LYS208 4.5 36.1 1.0 ZN B:ZN904 4.5 37.5 1.0 CA B:ASP171 4.5 35.0 1.0 C B:THR209 4.5 35.9 1.0 CG B:ASP311 4.5 38.3 1.0 NE2 B:HIS474 4.6 29.7 1.0 C B:ASP171 4.8 34.5 1.0 C25 B:6ZO907 4.8 60.7 1.0 C28 B:6ZO907 4.8 61.8 1.0 OD2 B:ASP311 4.8 35.4 1.0 O B:LYS208 4.9 36.1 1.0 N31 B:6ZO907 4.9 58.0 1.0 O B:THR209 4.9 35.3 1.0

S.B.Jones, L.A.Pfeifer, T.J.Bleisch, T.J.Beauchamp, J.D.Durbin, V.J.Klimkowski, N.E.Hughes, C.J.Rito, Y.Dao, J.M.Gruber, H.Bui, M.G.Chambers, S.Chandrasekhar, C.Lin, D.J.Mccann, D.R.Mudra, J.L.Oskins, C.A.Swearingen, K.Thirunavukkarasu, B.H.Norman. Novel Autotaxin Inhibitors For the Treatment of Osteoarthritis Pain: Lead Optimization Via Structure-Based Drug Design. Acs Med.Chem.Lett. V. 7 857 2016.
ISSN: ISSN 1948-5875
PubMed: 27660691
DOI: 10.1021/ACSMEDCHEMLETT.6B00207