Zinc in PDB 3nkm: Crystal Structure of Mouse Autotaxin

All present enzymatic activity of Crystal Structure of Mouse Autotaxin:
3.1.4.39;

The structure of Crystal Structure of Mouse Autotaxin, PDB code: 3nkm was solved by H.Nishimasu, R.Ishitani, E.Mihara, J.Takagi, J.Aoki, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.18 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.588, 94.731, 75.652, 90.00, 94.05, 90.00
R / Rfree (%)	16.3 / 21.3

The structure of Crystal Structure of Mouse Autotaxin also contains other interesting chemical elements:

Potassium	(K)	1 atom
Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Mouse Autotaxin (pdb code 3nkm). 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 Mouse Autotaxin, PDB code: 3nkm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Mouse Autotaxin


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 Mouse Autotaxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:21.6 occ:1.00 OG1 A:THR209 1.6 14.3 1.0 OD1 A:ASP171 1.9 13.3 1.0 NE2 A:HIS359 2.2 9.6 1.0 O2 A:SO41006 2.2 24.6 1.0 CG A:ASP171 2.7 13.5 1.0 CB A:THR209 2.8 18.6 1.0 OD2 A:ASP171 2.8 13.8 1.0 CD2 A:HIS359 3.0 12.5 1.0 CE1 A:HIS359 3.3 13.1 1.0 OD2 A:ASP358 3.3 19.6 1.0 S A:SO41006 3.4 28.1 1.0 O1 A:SO41006 3.5 13.9 1.0 OD1 A:ASP311 3.6 16.0 1.0 CA A:THR209 3.7 13.8 1.0 OD1 A:ASP358 3.8 15.4 1.0 CG2 A:THR209 3.8 15.2 1.0 CG A:ASP358 3.9 15.7 1.0 CG A:ASP311 3.9 17.6 1.0 N A:THR209 3.9 12.9 1.0 CB A:ASP171 4.0 14.5 1.0 N A:GLY172 4.1 11.7 1.0 CE1 A:HIS474 4.1 14.9 1.0 ZN A:ZN1002 4.1 13.7 1.0 CG A:HIS359 4.2 11.1 1.0 ND1 A:HIS359 4.3 11.5 1.0 O3 A:SO41006 4.3 18.6 1.0 NE2 A:HIS474 4.3 14.0 1.0 CB A:ASP311 4.3 15.1 1.0 OD2 A:ASP311 4.3 16.9 1.0 O4 A:SO41006 4.4 23.7 1.0 CA A:ASP171 4.4 14.2 1.0 C A:ASP171 4.4 12.7 1.0 CA A:GLY172 4.7 10.8 1.0 C A:LYS208 4.8 12.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Mouse Autotaxin


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 Mouse Autotaxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:13.7 occ:1.00 NE2 A:HIS315 2.0 11.4 1.0 NE2 A:HIS474 2.1 14.0 1.0 O3 A:SO41006 2.1 18.6 1.0 OD1 A:ASP311 2.1 16.0 1.0 OD2 A:ASP311 2.7 16.9 1.0 CG A:ASP311 2.7 17.6 1.0 CE1 A:HIS315 2.9 15.3 1.0 O2 A:SO41006 3.0 24.6 1.0 CD2 A:HIS315 3.0 16.0 1.0 S A:SO41006 3.0 28.1 1.0 CD2 A:HIS474 3.0 11.3 1.0 CE1 A:HIS474 3.1 14.9 1.0 O1 A:SO41006 3.7 13.9 1.0 ND1 A:HIS315 4.0 13.3 1.0 CG A:HIS315 4.1 16.0 1.0 ZN A:ZN1001 4.1 21.6 1.0 CE1 A:HIS359 4.2 13.1 1.0 ND1 A:HIS474 4.2 11.7 1.0 CG A:HIS474 4.2 7.7 1.0 NE2 A:HIS359 4.2 9.6 1.0 O4 A:SO41006 4.2 23.7 1.0 CB A:ASP311 4.2 15.1 1.0 CE A:MET361 4.5 10.6 1.0 OD1 A:ASP171 4.8 13.3 1.0 O A:HOH1529 4.8 27.6 1.0 O A:ASP311 4.9 13.2 1.0 OD1 A:ASP473 5.0 10.1 1.0

H.Nishimasu, S.Okudaira, K.Hama, E.Mihara, N.Dohmae, A.Inoue, R.Ishitani, J.Takagi, J.Aoki, O.Nureki. Crystal Structure of Autotaxin and Insight Into Gpcr Activation By Lipid Mediators Nat.Struct.Mol.Biol. V. 18 205 2011.
ISSN: ISSN 1545-9993
PubMed: 21240269
DOI: 10.1038/NSMB.1998