Atomistry » Zinc » PDB 5l03-5lbz » 5l0b
Atomistry »
  Zinc »
    PDB 5l03-5lbz »
      5l0b »

Zinc in PDB 5l0b: 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: 5l0b 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) 19.61 / 2.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.827, 96.733, 136.284, 90.00, 112.86, 90.00
R / Rfree (%) 17.6 / 20.9

Other elements in 5l0b:

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 5l0b). 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: 5l0b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5l0b

Go back to Zinc Binding Sites List in 5l0b
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:Zn912

b:29.4
occ:1.00
 OD1 A:ASP171 1.9 24.2 1.0
OG1 A:THR209 1.9 30.8 1.0
NE2 A:HIS359 2.0 21.3 1.0
OD2 A:ASP358 2.4 35.3 1.0
CG A:ASP171 2.6 27.4 1.0
OD2 A:ASP171 2.8 39.0 1.0
CD2 A:HIS359 2.9 21.3 1.0
CB A:THR209 3.0 32.9 1.0
CE1 A:HIS359 3.0 20.9 1.0
CG A:ASP358 3.1 28.9 1.0
OD1 A:ASP358 3.1 25.2 1.0
CA A:THR209 3.3 28.0 1.0
CG2 A:THR209 3.5 28.7 1.0
N A:THR209 3.8 27.1 1.0
O A:HOH1286 3.9 53.9 1.0
CB A:ASP171 3.9 24.1 1.0
O A:HOH1050 4.0 51.3 1.0
CG A:HIS359 4.0 21.9 1.0
ND1 A:HIS359 4.1 22.8 1.0
N A:GLY172 4.1 19.9 1.0
CA A:ASP171 4.3 23.9 1.0
OD1 A:ASP311 4.4 37.1 1.0
CB A:ASP358 4.5 23.5 1.0
CG A:ASP311 4.5 33.6 1.0
CE1 A:HIS474 4.5 26.5 1.0
C A:ASP171 4.6 26.0 1.0
C A:LYS208 4.7 28.4 1.0
ZN A:ZN913 4.7 32.5 1.0
C A:THR209 4.7 32.1 1.0
NE2 A:HIS474 4.7 27.5 1.0
OD2 A:ASP311 4.8 38.1 1.0
CB A:ASP311 4.9 22.8 1.0
CA A:GLY172 5.0 19.8 1.0

Zinc binding site 2 out of 6 in 5l0b

Go back to Zinc Binding Sites List in 5l0b
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:Zn913

b:32.5
occ:1.00
 O A:HOH1216 1.9 40.8 1.0
NE2 A:HIS315 2.0 29.9 1.0
NE2 A:HIS474 2.1 27.5 1.0
OD1 A:ASP311 2.1 37.1 1.0
OD2 A:ASP311 2.7 38.1 1.0
CG A:ASP311 2.7 33.6 1.0
CD2 A:HIS315 3.0 30.4 1.0
CE1 A:HIS315 3.0 29.6 1.0
CD2 A:HIS474 3.1 27.4 1.0
CE1 A:HIS474 3.1 26.5 1.0
O A:HOH1050 3.5 51.3 1.0
O A:HOH1314 3.9 58.4 1.0
O A:HOH1286 4.1 53.9 1.0
CE1 A:HIS359 4.1 20.9 1.0
CG A:HIS315 4.1 30.6 1.0
ND1 A:HIS315 4.1 31.4 1.0
CB A:ASP311 4.2 22.8 1.0
CG A:HIS474 4.2 25.3 1.0
ND1 A:HIS474 4.2 27.3 1.0
NE2 A:HIS359 4.4 21.3 1.0
CE A:MET361 4.5 25.9 1.0
OD1 A:ASP171 4.5 24.2 1.0
OG1 A:THR209 4.6 30.8 1.0
ZN A:ZN912 4.7 29.4 1.0
O A:ASP311 4.9 33.9 1.0

Zinc binding site 3 out of 6 in 5l0b

Go back to Zinc Binding Sites List in 5l0b
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:Zn914

b:53.9
occ:1.00
 OD1 A:ASN741 2.2 50.8 1.0
OD1 A:ASP739 2.3 40.2 1.0
O A:LEU745 2.4 31.5 1.0
OD1 A:ASP743 2.4 42.4 1.0
O A:HOH1160 2.4 46.6 1.0
OD1 A:ASP747 2.5 48.4 1.0
CG A:ASN741 3.2 51.6 1.0
CG A:ASP743 3.3 40.1 1.0
CG A:ASP739 3.4 39.0 1.0
C A:LEU745 3.5 32.3 1.0
ND2 A:ASN741 3.5 43.2 1.0
OD2 A:ASP743 3.6 45.6 1.0
CG A:ASP747 3.7 43.6 1.0
CA A:ASP739 3.9 30.2 1.0
N A:LEU745 4.0 27.9 1.0
N A:ASP747 4.1 34.5 1.0
C A:ARG746 4.1 37.1 1.0
CA A:LEU745 4.1 27.4 1.0
CB A:ASP739 4.1 32.0 1.0
O A:ARG746 4.2 38.1 1.0
CA A:ASP747 4.2 33.9 1.0
N A:ASP743 4.2 28.0 1.0
OD2 A:ASP739 4.4 40.0 1.0
CB A:LEU745 4.5 26.6 1.0
OD2 A:ASP747 4.5 41.5 1.0
O A:PHE738 4.5 27.6 1.0
C A:ASP739 4.5 35.7 1.0
CB A:ASP743 4.5 29.7 1.0
N A:ASN741 4.5 32.5 1.0
N A:ARG746 4.5 30.6 1.0
CB A:ASP747 4.5 34.5 1.0
CB A:ASN741 4.5 28.5 1.0
N A:TYR740 4.7 33.6 1.0
N A:TYR742 4.7 33.7 1.0
N A:GLY744 4.8 29.2 1.0
CA A:ASP743 4.8 28.4 1.0
CA A:ARG746 4.8 30.7 1.0
CA A:ASN741 4.9 32.5 1.0
C A:ASN741 4.9 37.6 1.0
OE2 A:GLU751 5.0 75.6 1.0

Zinc binding site 4 out of 6 in 5l0b

Go back to Zinc Binding Sites List in 5l0b
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:59.0
occ:1.00
 NE2 B:HIS315 2.1 76.4 1.0
NE2 B:HIS474 2.1 54.2 1.0
O B:HOH1161 2.1 40.3 1.0
OD1 B:ASP311 2.1 63.4 1.0
OD2 B:ASP311 2.7 74.9 1.0
CG B:ASP311 2.7 64.7 1.0
CD2 B:HIS315 3.1 76.8 1.0
CD2 B:HIS474 3.1 54.2 1.0
CE1 B:HIS315 3.1 76.1 1.0
CE1 B:HIS474 3.1 53.7 1.0
CE1 B:HIS359 4.1 49.8 1.0
CB B:ASP311 4.2 56.8 1.0
CG B:HIS315 4.2 75.2 1.0
CG B:HIS474 4.2 52.6 1.0
ND1 B:HIS315 4.2 76.7 1.0
ND1 B:HIS474 4.2 54.3 1.0
O B:HOH1231 4.4 50.9 1.0
NE2 B:HIS359 4.4 49.9 1.0
CE B:MET361 4.4 63.2 1.0
OD1 B:ASP171 4.5 55.7 1.0
OG1 B:THR209 4.6 41.5 1.0
ZN B:ZN910 4.6 55.8 1.0
O B:ASP311 5.0 62.0 1.0

Zinc binding site 5 out of 6 in 5l0b

Go back to Zinc Binding Sites List in 5l0b
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:55.8
occ:1.00
 OG1 B:THR209 1.9 41.5 1.0
OD1 B:ASP171 1.9 55.7 1.0
NE2 B:HIS359 2.0 49.9 1.0
OD2 B:ASP358 2.5 48.9 1.0
CG B:ASP171 2.7 55.1 1.0
CD2 B:HIS359 2.9 50.0 1.0
OD2 B:ASP171 2.9 61.7 1.0
CE1 B:HIS359 2.9 49.8 1.0
CB B:THR209 2.9 42.1 1.0
CG B:ASP358 3.1 43.4 1.0
OD1 B:ASP358 3.2 41.8 1.0
CA B:THR209 3.3 37.5 1.0
CG2 B:THR209 3.5 37.2 1.0
N B:THR209 3.7 37.4 1.0
CG B:HIS359 4.0 48.9 1.0
ND1 B:HIS359 4.0 50.9 1.0
CB B:ASP171 4.0 45.0 1.0
N B:GLY172 4.1 42.6 1.0
CA B:ASP171 4.4 42.8 1.0
OD1 B:ASP311 4.4 63.4 1.0
CE1 B:HIS474 4.5 53.7 1.0
CG B:ASP311 4.5 64.7 1.0
CB B:ASP358 4.5 43.1 1.0
ZN B:ZN909 4.6 59.0 1.0
C B:LYS208 4.6 40.0 1.0
NE2 B:HIS474 4.7 54.2 1.0
C B:ASP171 4.7 46.4 1.0
C B:THR209 4.7 43.3 1.0
OD2 B:ASP311 4.9 74.9 1.0
CB B:ASP311 4.9 56.8 1.0
CA B:GLY172 5.0 42.8 1.0

Zinc binding site 6 out of 6 in 5l0b

Go back to Zinc Binding Sites List in 5l0b
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:52.5
occ:1.00
 OD1 B:ASN741 2.1 56.8 1.0
OD1 B:ASP739 2.4 34.1 1.0
O B:HOH1066 2.4 44.0 1.0
O B:LEU745 2.5 30.6 1.0
OD1 B:ASP747 2.5 41.3 1.0
OD1 B:ASP743 2.5 43.9 1.0
CG B:ASN741 3.1 55.5 1.0
CG B:ASP743 3.3 42.1 1.0
ND2 B:ASN741 3.4 48.8 1.0
CG B:ASP739 3.5 31.2 1.0
C B:LEU745 3.6 29.7 1.0
CG B:ASP747 3.6 37.5 1.0
OD2 B:ASP743 3.7 47.4 1.0
CA B:ASP739 4.0 24.6 1.0
N B:LEU745 4.1 28.3 1.0
N B:ASP747 4.1 32.6 1.0
C B:ARG746 4.2 33.8 1.0
O B:ARG746 4.2 34.8 1.0
CB B:ASP739 4.2 26.6 1.0
CA B:LEU745 4.2 27.4 1.0
CA B:ASP747 4.2 32.7 1.0
N B:ASP743 4.3 30.9 1.0
OD2 B:ASP747 4.4 40.6 1.0
OD2 B:ASP739 4.5 30.1 1.0
N B:ASN741 4.5 34.6 1.0
CB B:ASN741 4.5 35.3 1.0
CB B:ASP747 4.5 32.6 1.0
C B:ASP739 4.5 33.8 1.0
CB B:LEU745 4.5 27.8 1.0
O B:PHE738 4.5 26.7 1.0
CB B:ASP743 4.5 32.8 1.0
N B:ARG746 4.6 27.2 1.0
N B:TYR740 4.7 33.7 1.0
N B:TYR742 4.7 36.4 1.0
CA B:ASN741 4.8 35.2 1.0
OE2 B:GLU751 4.8 75.7 1.0
CA B:ASP743 4.8 31.7 1.0
N B:GLY744 4.9 31.8 1.0
CA B:ARG746 4.9 26.7 1.0
C B:ASN741 4.9 40.6 1.0
OE1 B:GLU751 5.0 70.8 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: Sun Oct 27 20:44:26 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy