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Zinc in PDB 3way: Crystal Structure of Autotaxin in Complex with 4BOA

Enzymatic activity of Crystal Structure of Autotaxin in Complex with 4BOA

All present enzymatic activity of Crystal Structure of Autotaxin in Complex with 4BOA:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin in Complex with 4BOA, PDB code: 3way 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) 49.23 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.556, 94.524, 75.242, 90.00, 93.98, 90.00
R / Rfree (%) 18.1 / 22.1

Other elements in 3way:

The structure of Crystal Structure of Autotaxin in Complex with 4BOA also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 4 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Autotaxin in Complex with 4BOA (pdb code 3way). 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 4BOA, PDB code: 3way:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3way

Go back to Zinc Binding Sites List in 3way
Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin in Complex with 4BOA


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 4BOA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn911

b:16.0
occ:1.00
OD1 A:ASP171 1.9 16.3 1.0
OG1 A:THR209 2.0 13.1 1.0
OD2 A:ASP358 2.1 13.9 1.0
NE2 A:HIS359 2.1 13.1 1.0
OBE A:DWY931 2.6 16.8 0.7
CG A:ASP171 2.7 15.5 1.0
OBE A:DWY931 2.7 16.9 0.3
OD2 A:ASP171 2.8 17.8 1.0
CG A:ASP358 2.9 12.5 1.0
BBC A:DWY931 2.9 35.1 0.7
CD2 A:HIS359 2.9 11.8 1.0
BBC A:DWY931 3.1 33.9 0.3
CE1 A:HIS359 3.1 13.6 1.0
OD1 A:ASP358 3.1 13.1 1.0
CB A:THR209 3.2 13.8 1.0
CA A:THR209 3.5 12.8 1.0
CG2 A:THR209 3.6 12.7 1.0
N A:THR209 3.9 12.3 1.0
OBD A:DWY931 3.9 15.2 0.7
CAX A:DWY931 4.0 17.8 0.3
CB A:ASP171 4.0 14.1 1.0
CAX A:DWY931 4.0 17.8 0.7
CAY A:DWY931 4.0 16.5 0.3
CG A:HIS359 4.1 11.6 1.0
CAY A:DWY931 4.1 16.4 0.7
ND1 A:HIS359 4.1 11.2 1.0
N A:GLY172 4.1 12.6 1.0
OBD A:DWY931 4.1 17.0 0.3
OD1 A:ASP311 4.3 17.8 1.0
CE1 A:HIS474 4.3 15.1 1.0
CB A:ASP358 4.3 14.5 1.0
CG A:ASP311 4.4 15.7 1.0
CA A:ASP171 4.4 13.6 1.0
OD2 A:ASP311 4.5 16.9 1.0
ZN A:ZN912 4.6 16.0 1.0
C A:ASP171 4.6 17.1 1.0
NE2 A:HIS474 4.6 14.4 1.0
C A:LYS208 4.6 14.4 1.0
C A:THR209 4.8 11.9 1.0
CA A:GLY172 4.9 15.8 1.0
CB A:ASP311 4.9 15.7 1.0

Zinc binding site 2 out of 2 in 3way

Go back to Zinc Binding Sites List in 3way
Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin in Complex with 4BOA


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 4BOA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn912

b:16.0
occ:1.00
NE2 A:HIS474 2.0 14.4 1.0
OD2 A:ASP311 2.1 16.9 1.0
NE2 A:HIS315 2.1 15.6 1.0
OBE A:DWY931 2.2 16.9 0.3
OBE A:DWY931 2.3 16.8 0.7
OD1 A:ASP311 2.7 17.8 1.0
CG A:ASP311 2.7 15.7 1.0
CE1 A:HIS474 3.0 15.1 1.0
CD2 A:HIS474 3.1 11.9 1.0
CD2 A:HIS315 3.1 17.4 1.0
CE1 A:HIS315 3.1 15.3 1.0
BBC A:DWY931 3.2 33.9 0.3
BBC A:DWY931 3.3 35.1 0.7
OBD A:DWY931 3.6 17.0 0.3
OBD A:DWY931 3.8 15.2 0.7
ND1 A:HIS474 4.1 11.4 1.0
CG A:HIS474 4.2 11.1 1.0
CB A:ASP311 4.2 15.7 1.0
ND1 A:HIS315 4.2 15.1 1.0
CG A:HIS315 4.2 16.7 1.0
CE1 A:HIS359 4.3 13.6 1.0
CAY A:DWY931 4.3 16.5 0.3
CAY A:DWY931 4.4 16.4 0.7
NE2 A:HIS359 4.5 13.1 1.0
OD1 A:ASP171 4.6 16.3 1.0
ZN A:ZN911 4.6 16.0 1.0
CE A:MET361 4.6 15.7 1.0
O A:HOH1350 4.6 22.9 1.0
CAX A:DWY931 4.6 17.8 0.7
CAX A:DWY931 4.6 17.8 0.3
OG1 A:THR209 4.8 13.1 1.0
O A:ASP311 5.0 18.0 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 04:57:11 2020

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