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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

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