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:
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: Sun Oct 27 20:44:26 2024
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