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Zinc in PDB 5l0e: Crystal Structure of Autotaxin and Compound 1

Enzymatic activity of Crystal Structure of Autotaxin and Compound 1

All present enzymatic activity of Crystal Structure of Autotaxin and Compound 1:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin and Compound 1, PDB code: 5l0e 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) 19.98 / 3.06
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.175, 96.838, 136.917, 90.00, 112.82, 90.00
R / Rfree (%) 18.3 / 21.1

Other elements in 5l0e:

The structure of Crystal Structure of Autotaxin and Compound 1 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Autotaxin and Compound 1 (pdb code 5l0e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Autotaxin and Compound 1, PDB code: 5l0e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5l0e

Go back to Zinc Binding Sites List in 5l0e
Zinc binding site 1 out of 6 in the Crystal Structure of Autotaxin and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn913

b:61.9
occ:0.50
 OG1 A:THR209 1.9 45.1 1.0
OD1 A:ASP171 1.9 41.7 1.0
NE2 A:HIS359 1.9 34.8 1.0
CE1 A:HIS359 2.7 34.3 1.0
CG A:ASP171 2.8 44.4 1.0
OD2 A:ASP171 3.1 52.6 1.0
CD2 A:HIS359 3.1 35.4 1.0
CB A:THR209 3.1 44.5 1.0
OD2 A:ASP358 3.2 52.0 1.0
CA A:THR209 3.6 34.9 1.0
CG2 A:THR209 3.8 41.2 1.0
OD1 A:ASP358 3.8 54.1 1.0
OD1 A:ASP311 3.8 23.7 1.0
CG A:ASP358 3.8 49.8 1.0
ZN A:ZN914 3.9 30.8 1.0
N A:THR209 3.9 35.3 1.0
ND1 A:HIS359 3.9 35.3 1.0
C6 A:6ZN911 3.9 60.6 1.0
CG A:ASP311 3.9 25.7 1.0
N29 A:6ZN911 3.9 60.8 1.0
CE1 A:HIS474 4.0 31.6 1.0
NE2 A:HIS474 4.0 32.0 1.0
CG A:HIS359 4.1 34.2 1.0
C13 A:6ZN911 4.1 60.9 1.0
CB A:ASP171 4.2 35.8 1.0
OD2 A:ASP311 4.2 37.4 1.0
N A:GLY172 4.3 31.7 1.0
CB A:ASP311 4.5 20.7 1.0
CA A:ASP171 4.7 34.1 1.0
C A:LYS208 4.8 38.3 1.0
C A:ASP171 4.8 37.7 1.0
ND1 A:HIS474 4.9 32.8 1.0
C3 A:6ZN911 4.9 60.4 1.0
CA A:GLY172 4.9 30.3 1.0
CD2 A:HIS474 5.0 32.3 1.0
C17 A:6ZN911 5.0 61.1 1.0

Zinc binding site 2 out of 6 in 5l0e

Go back to Zinc Binding Sites List in 5l0e
Zinc binding site 2 out of 6 in the Crystal Structure of Autotaxin and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn914

b:30.8
occ:1.00
 N29 A:6ZN911 1.9 60.8 1.0
NE2 A:HIS315 2.0 26.5 1.0
NE2 A:HIS474 2.3 32.0 1.0
OD1 A:ASP311 2.4 23.7 1.0
C17 A:6ZN911 2.6 61.1 1.0
OD2 A:ASP311 2.6 37.4 1.0
O32 A:6ZN911 2.7 60.0 1.0
CG A:ASP311 2.8 25.7 1.0
CD2 A:HIS315 3.0 27.0 1.0
CE1 A:HIS315 3.1 26.1 1.0
C13 A:6ZN911 3.1 60.9 1.0
CE1 A:HIS474 3.2 31.6 1.0
CD2 A:HIS474 3.3 32.3 1.0
C6 A:6ZN911 3.8 60.6 1.0
ZN A:ZN913 3.9 61.9 0.5
O34 A:6ZN911 3.9 61.7 1.0
C14 A:6ZN911 4.0 61.0 1.0
CG A:HIS315 4.2 25.6 1.0
ND1 A:HIS315 4.2 27.1 1.0
CE1 A:HIS359 4.3 34.3 1.0
CB A:ASP311 4.3 20.7 1.0
ND1 A:HIS474 4.4 32.8 1.0
OG1 A:THR209 4.4 45.1 1.0
CG A:HIS474 4.4 31.0 1.0
NE2 A:HIS359 4.5 34.8 1.0
OD1 A:ASP171 4.5 41.7 1.0
CE A:MET361 4.8 40.7 1.0

Zinc binding site 3 out of 6 in 5l0e

Go back to Zinc Binding Sites List in 5l0e
Zinc binding site 3 out of 6 in the Crystal Structure of Autotaxin and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn915

b:72.2
occ:1.00
 OD1 A:ASN741 2.2 61.6 1.0
OD1 A:ASP743 2.3 48.1 1.0
O A:LEU745 2.4 44.2 1.0
OD1 A:ASP747 2.5 64.0 1.0
OD1 A:ASP739 2.6 43.0 1.0
CG A:ASN741 3.1 53.4 1.0
CG A:ASP743 3.2 47.6 1.0
O A:HOH1007 3.2 52.6 1.0
ND2 A:ASN741 3.4 32.9 1.0
OD2 A:ASP743 3.5 54.9 1.0
C A:LEU745 3.5 43.6 1.0
CG A:ASP739 3.7 43.0 1.0
CG A:ASP747 3.7 63.4 1.0
O A:ARG746 4.0 50.7 1.0
N A:ASP747 4.1 51.5 1.0
C A:ARG746 4.1 51.0 1.0
N A:LEU745 4.1 38.1 1.0
CA A:LEU745 4.2 37.0 1.0
CA A:ASP747 4.2 51.9 1.0
CA A:ASP739 4.2 36.1 1.0
N A:ASP743 4.4 36.2 1.0
CB A:LEU745 4.4 35.9 1.0
CB A:ASP743 4.4 37.4 1.0
CB A:ASP739 4.5 36.5 1.0
N A:ARG746 4.5 41.0 1.0
CB A:ASN741 4.5 36.3 1.0
CB A:ASP747 4.5 53.3 1.0
OD2 A:ASP747 4.6 69.2 1.0
N A:ASN741 4.6 41.0 1.0
OD2 A:ASP739 4.6 47.2 1.0
O A:PHE738 4.7 39.7 1.0
OE2 A:GLU751 4.7 0.1 1.0
C A:ASP739 4.8 44.0 1.0
CA A:ARG746 4.8 41.7 1.0
OE1 A:GLU751 4.8 0.1 1.0
CA A:ASP743 4.9 36.2 1.0
N A:TYR740 4.9 40.5 1.0
N A:TYR742 4.9 41.0 1.0
N A:GLY744 4.9 39.9 1.0
CA A:ASN741 4.9 40.3 1.0
CD A:GLU751 5.0 0.5 1.0

Zinc binding site 4 out of 6 in 5l0e

Go back to Zinc Binding Sites List in 5l0e
Zinc binding site 4 out of 6 in the Crystal Structure of Autotaxin and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn909

b:35.4
occ:1.00
 N29 B:6ZN908 1.9 52.3 1.0
NE2 B:HIS315 2.1 56.7 1.0
OD1 B:ASP311 2.1 34.3 1.0
NE2 B:HIS474 2.2 32.5 1.0
OD2 B:ASP311 2.5 39.0 1.0
CG B:ASP311 2.6 34.5 1.0
C17 B:6ZN908 2.8 51.5 1.0
O32 B:6ZN908 2.9 48.8 1.0
C13 B:6ZN908 3.1 52.2 1.0
CD2 B:HIS315 3.1 56.6 1.0
CD2 B:HIS474 3.2 32.9 1.0
CE1 B:HIS315 3.2 56.5 1.0
CE1 B:HIS474 3.2 31.9 1.0
C6 B:6ZN908 3.7 50.4 1.0
O34 B:6ZN908 4.0 53.2 1.0
C14 B:6ZN908 4.1 54.4 1.0
CE1 B:HIS359 4.1 36.5 1.0
CB B:ASP311 4.1 33.1 1.0
CG B:HIS315 4.2 54.8 1.0
ND1 B:HIS315 4.3 56.7 1.0
CG B:HIS474 4.3 31.5 1.0
NE2 B:HIS359 4.4 37.0 1.0
ND1 B:HIS474 4.4 33.1 1.0
OD1 B:ASP171 4.4 57.9 1.0
OG1 B:THR209 4.5 49.7 1.0
CE B:MET361 4.5 37.0 1.0
ZN B:ZN910 4.6 89.8 1.0
O B:ASP311 5.0 38.7 1.0

Zinc binding site 5 out of 6 in 5l0e

Go back to Zinc Binding Sites List in 5l0e
Zinc binding site 5 out of 6 in the Crystal Structure of Autotaxin and Compound 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Autotaxin and Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn910

b:89.8
occ:1.00
 OG1 B:THR209 1.9 49.7 1.0
NE2 B:HIS359 2.0 37.0 1.0
OD1 B:ASP171 2.1 57.9 1.0
OD2 B:ASP358 2.4 69.3 1.0
CG B:ASP171 2.8 55.1 1.0
CB B:THR209 2.9 42.3 1.0
CD2 B:HIS359 2.9 37.4 1.0
OD2 B:ASP171 2.9 61.3 1.0
CE1 B:HIS359 3.0 36.5 1.0
CG B:ASP358 3.1 58.5 1.0
CA B:THR209 3.2 33.6 1.0
OD1 B:ASP358 3.2 58.0 1.0
CG2 B:THR209 3.3 37.2 1.0
N B:THR209 3.7 33.7 1.0
CG B:HIS359 4.0 36.0 1.0
ND1 B:HIS359 4.1 37.4 1.0
CB B:ASP171 4.1 38.9 1.0
N B:GLY172 4.3 35.6 1.0
CB B:ASP358 4.5 45.3 1.0
CE1 B:HIS474 4.5 31.9 1.0
CA B:ASP171 4.5 37.2 1.0
OD1 B:ASP311 4.5 34.3 1.0
C B:LYS208 4.6 36.1 1.0
C B:THR209 4.6 36.3 1.0
ZN B:ZN909 4.6 35.4 1.0
C6 B:6ZN908 4.6 50.4 1.0
CG B:ASP311 4.7 34.5 1.0
NE2 B:HIS474 4.7 32.5 1.0
C13 B:6ZN908 4.8 52.2 1.0
N29 B:6ZN908 4.8 52.3 1.0
C B:ASP171 4.8 40.0 1.0
O B:THR209 5.0 36.5 1.0
OD2 B:ASP311 5.0 39.0 1.0

Zinc binding site 6 out of 6 in 5l0e

Go back to Zinc Binding Sites List in 5l0e
Zinc binding site 6 out of 6 in the Crystal Structure of Autotaxin and Compound 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Autotaxin and Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn911

b:74.8
occ:1.00
 OD1 B:ASN741 2.3 58.6 1.0
O B:LEU745 2.4 36.3 1.0
OD1 B:ASP747 2.5 53.4 1.0
OD1 B:ASP743 2.5 48.0 1.0
OD1 B:ASP739 2.8 34.2 1.0
CG B:ASN741 3.2 58.5 1.0
CG B:ASP743 3.3 48.5 1.0
ND2 B:ASN741 3.3 49.8 1.0
C B:LEU745 3.4 35.9 1.0
OD2 B:ASP743 3.5 54.1 1.0
CG B:ASP747 3.7 52.9 1.0
O B:ARG746 3.8 44.5 1.0
C B:ARG746 3.9 42.6 1.0
N B:ASP747 3.9 40.7 1.0
CG B:ASP739 4.0 33.7 1.0
CA B:ASP747 4.0 41.1 1.0
N B:LEU745 4.2 33.8 1.0
CA B:LEU745 4.2 32.7 1.0
CB B:LEU745 4.4 32.8 1.0
N B:ARG746 4.4 32.6 1.0
CB B:ASP747 4.4 41.8 1.0
CA B:ASP739 4.4 24.1 1.0
OE2 B:GLU751 4.5 76.3 1.0
OD2 B:ASP747 4.6 59.9 1.0
OE1 B:GLU751 4.6 66.7 1.0
CB B:ASP743 4.6 37.9 1.0
CB B:ASN741 4.6 32.7 1.0
CB B:ASP739 4.6 25.0 1.0
N B:ASP743 4.6 35.1 1.0
CA B:ARG746 4.7 33.3 1.0
O B:PHE738 4.7 34.6 1.0
CD B:GLU751 4.7 79.4 1.0
N B:ASN741 4.8 37.5 1.0
OD2 B:ASP739 4.9 38.9 1.0
C B:ASP739 4.9 30.9 1.0

Reference:

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
Page generated: Wed Dec 16 06:28:09 2020

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