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Zinc in PDB 3wav: Crystal Structure of Autotaxin in Complex with Compound 10

Enzymatic activity of Crystal Structure of Autotaxin in Complex with Compound 10

All present enzymatic activity of Crystal Structure of Autotaxin in Complex with Compound 10:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin in Complex with Compound 10, PDB code: 3wav was solved by H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.24 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.505, 94.015, 75.446, 90.00, 94.52, 90.00
R / Rfree (%) 18.8 / 22.3

Other elements in 3wav:

The structure of Crystal Structure of Autotaxin in Complex with Compound 10 also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Autotaxin in Complex with Compound 10 (pdb code 3wav). 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 in Complex with Compound 10, PDB code: 3wav:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3wav

Go back to Zinc Binding Sites List in 3wav
Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin in Complex with Compound 10


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 in Complex with Compound 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn911

b:24.0
occ:1.00
OD1 A:ASP171 1.9 19.3 1.0
OG1 A:THR209 2.1 28.4 1.0
NE2 A:HIS359 2.1 15.2 1.0
OD2 A:ASP358 2.4 27.0 1.0
CG A:ASP171 2.6 18.3 1.0
OD2 A:ASP171 2.8 22.9 1.0
CD2 A:HIS359 3.0 14.3 1.0
CE1 A:HIS359 3.1 18.5 1.0
CB A:THR209 3.1 21.4 1.0
O1 A:SO4936 3.2 37.8 1.0
CG A:ASP358 3.2 20.4 1.0
OD1 A:ASP358 3.4 19.0 1.0
CG2 A:THR209 3.5 22.4 1.0
CA A:THR209 3.5 16.9 1.0
O2 A:SO4936 3.8 23.4 1.0
N A:THR209 3.9 14.7 1.0
OD1 A:ASP311 3.9 20.4 1.0
CB A:ASP171 4.0 14.8 1.0
CG A:HIS359 4.1 16.4 1.0
ND1 A:HIS359 4.1 13.5 1.0
N A:GLY172 4.1 15.0 1.0
S A:SO4936 4.2 34.7 1.0
CG A:ASP311 4.2 23.7 1.0
CE1 A:HIS474 4.3 19.3 1.0
CA A:ASP171 4.4 15.2 1.0
ZN A:ZN912 4.4 18.5 1.0
C A:ASP171 4.5 18.0 1.0
NE2 A:HIS474 4.6 18.8 1.0
CB A:ASP358 4.7 19.7 1.0
CB A:ASP311 4.7 21.2 1.0
C A:LYS208 4.7 18.4 1.0
CA A:GLY172 4.7 17.2 1.0
OD2 A:ASP311 4.8 24.6 1.0
C A:THR209 4.9 15.4 1.0

Zinc binding site 2 out of 2 in 3wav

Go back to Zinc Binding Sites List in 3wav
Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin in Complex with Compound 10


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 in Complex with Compound 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn912

b:18.5
occ:1.00
NE2 A:HIS474 1.9 18.8 1.0
NE2 A:HIS315 2.0 21.0 1.0
OD1 A:ASP311 2.1 20.4 1.0
O1 A:SO4936 2.5 37.8 1.0
O3 A:SO4936 2.5 40.1 1.0
OD2 A:ASP311 2.7 24.6 1.0
CG A:ASP311 2.7 23.7 1.0
CE1 A:HIS474 2.9 19.3 1.0
CD2 A:HIS474 3.0 15.8 1.0
CD2 A:HIS315 3.0 20.3 1.0
S A:SO4936 3.0 34.7 1.0
CE1 A:HIS315 3.0 22.9 1.0
O2 A:SO4936 3.9 23.4 1.0
ND1 A:HIS474 4.0 15.7 1.0
CE1 A:HIS359 4.1 18.5 1.0
CG A:HIS474 4.1 17.5 1.0
ND1 A:HIS315 4.1 22.1 1.0
CG A:HIS315 4.1 22.9 1.0
O4 A:SO4936 4.2 32.6 1.0
CB A:ASP311 4.2 21.2 1.0
NE2 A:HIS359 4.3 15.2 1.0
CE A:MET361 4.4 14.4 1.0
ZN A:ZN911 4.4 24.0 1.0
O A:HOH1335 4.6 34.2 1.0
OD1 A:ASP171 4.6 19.3 1.0
OG1 A:THR209 4.7 28.4 1.0
O A:ASP311 4.8 20.1 1.0

Reference:

M.Kawaguchi, T.Okabe, S.Okudaira, H.Nishimasu, R.Ishitani, H.Kojima, O.Nureki, J.Aoki, T.Nagano. Screening and X-Ray Crystal Structure-Based Optimization of Autotaxin (ENPP2) Inhibitors, Using A Newly Developed Fluorescence Probe Acs Chem.Biol. V. 8 1713 2013.
ISSN: ISSN 1554-8929
PubMed: 23688339
DOI: 10.1021/CB400150C
Page generated: Wed Dec 16 04:57:08 2020

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