Zinc in PDB 7mfh: Crystal Structure of Bio-32546 Bound Mouse Autotaxin
Enzymatic activity of Crystal Structure of Bio-32546 Bound Mouse Autotaxin
All present enzymatic activity of Crystal Structure of Bio-32546 Bound Mouse Autotaxin:
3.1.4.39;
Protein crystallography data
The structure of Crystal Structure of Bio-32546 Bound Mouse Autotaxin, PDB code: 7mfh
was solved by
J.V.Chodaparambil,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.13 /
2.30
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.02,
61.62,
67.32,
89.07,
74.2,
79.88
|
R / Rfree (%)
|
21.5 /
26.8
|
Other elements in 7mfh:
The structure of Crystal Structure of Bio-32546 Bound Mouse Autotaxin also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin
(pdb code 7mfh). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the
Crystal Structure of Bio-32546 Bound Mouse Autotaxin, PDB code: 7mfh:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
Zinc binding site 1 out
of 7 in 7mfh
Go back to
Zinc Binding Sites List in 7mfh
Zinc binding site 1 out
of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin
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 Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn904
b:66.5
occ:1.00
|
OD1
|
A:ASP739
|
2.4
|
46.5
|
1.0
|
OD1
|
A:ASN741
|
2.4
|
46.0
|
1.0
|
OD1
|
A:ASP747
|
2.5
|
45.0
|
1.0
|
OD1
|
A:ASN743
|
2.5
|
44.5
|
1.0
|
O
|
A:HOH1012
|
2.6
|
40.4
|
1.0
|
O
|
A:LEU745
|
2.6
|
47.5
|
1.0
|
CG
|
A:ASN743
|
3.3
|
46.6
|
1.0
|
CG
|
A:ASP739
|
3.3
|
48.9
|
1.0
|
CG
|
A:ASN741
|
3.4
|
53.2
|
1.0
|
C
|
A:LEU745
|
3.5
|
36.0
|
1.0
|
ND2
|
A:ASN743
|
3.6
|
46.1
|
1.0
|
CG
|
A:ASP747
|
3.6
|
51.0
|
1.0
|
ND2
|
A:ASN741
|
3.7
|
58.1
|
1.0
|
CA
|
A:ASP739
|
3.8
|
41.2
|
1.0
|
CB
|
A:ASP739
|
3.9
|
48.9
|
1.0
|
N
|
A:ASP747
|
4.1
|
50.1
|
1.0
|
N
|
A:LEU745
|
4.1
|
45.0
|
1.0
|
C
|
A:ARG746
|
4.1
|
45.9
|
1.0
|
OE1
|
A:GLU751
|
4.1
|
49.0
|
1.0
|
OD2
|
A:ASP739
|
4.2
|
45.1
|
1.0
|
CA
|
A:ASP747
|
4.2
|
37.6
|
1.0
|
O
|
A:ARG746
|
4.2
|
52.0
|
1.0
|
CA
|
A:LEU745
|
4.2
|
44.2
|
1.0
|
N
|
A:ASN743
|
4.4
|
47.4
|
1.0
|
N
|
A:ARG746
|
4.4
|
37.5
|
1.0
|
C
|
A:ASP739
|
4.4
|
51.1
|
1.0
|
CB
|
A:LEU745
|
4.4
|
37.9
|
1.0
|
OD2
|
A:ASP747
|
4.5
|
53.0
|
1.0
|
O
|
A:PHE738
|
4.5
|
47.1
|
1.0
|
N
|
A:TYR740
|
4.5
|
49.6
|
1.0
|
N
|
A:ASN741
|
4.5
|
42.0
|
1.0
|
CB
|
A:ASP747
|
4.5
|
51.3
|
1.0
|
CB
|
A:ASN743
|
4.6
|
37.2
|
1.0
|
CB
|
A:ASN741
|
4.7
|
43.5
|
1.0
|
CA
|
A:ARG746
|
4.7
|
41.8
|
1.0
|
N
|
A:TYR742
|
4.8
|
45.0
|
1.0
|
CA
|
A:ASN743
|
4.9
|
49.2
|
1.0
|
CA
|
A:ASN741
|
4.9
|
45.4
|
1.0
|
C
|
A:ASN741
|
5.0
|
43.7
|
1.0
|
N
|
A:ASP739
|
5.0
|
47.1
|
1.0
|
|
Zinc binding site 2 out
of 7 in 7mfh
Go back to
Zinc Binding Sites List in 7mfh
Zinc binding site 2 out
of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin
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 Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn912
b:50.8
occ:1.00
|
OD1
|
A:ASP311
|
2.2
|
52.9
|
1.0
|
OD2
|
A:ASP311
|
2.3
|
56.0
|
1.0
|
NE2
|
A:HIS315
|
2.3
|
57.5
|
1.0
|
O
|
A:HOH1156
|
2.3
|
55.5
|
1.0
|
NE2
|
A:HIS474
|
2.3
|
63.2
|
1.0
|
CG
|
A:ASP311
|
2.6
|
45.2
|
1.0
|
CD2
|
A:HIS315
|
3.1
|
44.8
|
1.0
|
CD2
|
A:HIS474
|
3.2
|
45.5
|
1.0
|
CE1
|
A:HIS474
|
3.3
|
55.4
|
1.0
|
CE1
|
A:HIS315
|
3.4
|
47.6
|
1.0
|
O
|
A:HOH1026
|
3.5
|
47.8
|
1.0
|
OG1
|
A:THR209
|
3.9
|
63.4
|
1.0
|
CB
|
A:ASP311
|
4.0
|
55.1
|
1.0
|
CE1
|
A:HIS359
|
4.1
|
49.4
|
1.0
|
CG
|
A:HIS315
|
4.3
|
50.2
|
1.0
|
OD2
|
A:ASP171
|
4.3
|
77.4
|
1.0
|
ND1
|
A:HIS474
|
4.4
|
45.9
|
1.0
|
CG
|
A:HIS474
|
4.4
|
58.4
|
1.0
|
ND1
|
A:HIS315
|
4.4
|
61.0
|
1.0
|
NE2
|
A:HIS359
|
4.4
|
64.5
|
1.0
|
O
|
A:ASP311
|
4.8
|
62.6
|
1.0
|
OD1
|
A:ASP171
|
4.9
|
58.7
|
1.0
|
CG
|
A:ASP171
|
4.9
|
61.9
|
1.0
|
CA
|
A:ASP311
|
5.0
|
50.3
|
1.0
|
|
Zinc binding site 3 out
of 7 in 7mfh
Go back to
Zinc Binding Sites List in 7mfh
Zinc binding site 3 out
of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin
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 Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn913
b:68.5
occ:1.00
|
OE2
|
A:GLU847
|
1.9
|
108.8
|
1.0
|
CD
|
A:GLU847
|
3.1
|
109.9
|
1.0
|
N
|
A:LEU788
|
3.3
|
46.3
|
1.0
|
CA
|
A:PRO787
|
3.8
|
58.3
|
1.0
|
CG
|
A:GLU847
|
3.8
|
109.4
|
1.0
|
CB
|
A:PRO787
|
4.1
|
52.9
|
1.0
|
OE1
|
A:GLU847
|
4.1
|
111.6
|
1.0
|
C
|
A:PRO787
|
4.1
|
64.9
|
1.0
|
O
|
A:LEU788
|
4.1
|
53.1
|
1.0
|
CD1
|
A:LEU851
|
4.2
|
43.1
|
1.0
|
CA
|
A:LEU788
|
4.3
|
52.7
|
1.0
|
CG
|
A:ARG843
|
4.3
|
70.5
|
1.0
|
O
|
A:GLU847
|
4.3
|
59.3
|
1.0
|
CB
|
A:LEU788
|
4.4
|
42.7
|
1.0
|
CB
|
A:LEU851
|
4.4
|
45.3
|
1.0
|
CG
|
A:LEU788
|
4.4
|
60.2
|
1.0
|
CD2
|
A:LEU851
|
4.5
|
56.1
|
1.0
|
CD1
|
A:ILE848
|
4.5
|
53.3
|
1.0
|
CG
|
A:LEU851
|
4.6
|
59.6
|
1.0
|
C
|
A:LEU788
|
4.6
|
55.6
|
1.0
|
CB
|
A:GLU847
|
4.7
|
108.8
|
1.0
|
C
|
A:GLU847
|
4.7
|
54.1
|
1.0
|
NE
|
A:ARG843
|
4.9
|
59.3
|
1.0
|
CD1
|
A:LEU788
|
4.9
|
42.0
|
1.0
|
CB
|
A:ARG843
|
4.9
|
72.9
|
1.0
|
CD
|
A:ARG843
|
4.9
|
58.0
|
1.0
|
|
Zinc binding site 4 out
of 7 in 7mfh
Go back to
Zinc Binding Sites List in 7mfh
Zinc binding site 4 out
of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin
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 Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn919
b:90.3
occ:1.00
|
ND1
|
A:HIS281
|
2.3
|
71.0
|
1.0
|
CE1
|
A:HIS281
|
2.8
|
77.0
|
1.0
|
OG
|
A:SER307
|
3.0
|
62.9
|
1.0
|
CG
|
A:HIS281
|
3.5
|
60.4
|
1.0
|
OG1
|
A:THR334
|
3.6
|
50.7
|
1.0
|
CB
|
A:SER307
|
3.7
|
59.0
|
1.0
|
CZ
|
A:PHE305
|
3.9
|
54.2
|
1.0
|
NE2
|
A:HIS281
|
4.1
|
63.8
|
1.0
|
CB
|
A:HIS281
|
4.2
|
55.6
|
1.0
|
CE1
|
A:PHE305
|
4.2
|
57.4
|
1.0
|
CB
|
A:THR334
|
4.3
|
48.4
|
1.0
|
CG2
|
A:THR334
|
4.4
|
44.3
|
1.0
|
CD2
|
A:HIS281
|
4.4
|
62.3
|
1.0
|
CA
|
A:ILE331
|
4.8
|
53.2
|
1.0
|
CA
|
A:SER307
|
4.8
|
61.4
|
1.0
|
CG1
|
A:ILE331
|
4.8
|
72.9
|
1.0
|
O
|
A:GLU330
|
4.9
|
58.9
|
1.0
|
|
Zinc binding site 5 out
of 7 in 7mfh
Go back to
Zinc Binding Sites List in 7mfh
Zinc binding site 5 out
of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin
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 Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn920
b:44.5
occ:1.00
|
O
|
A:HOH1063
|
2.1
|
63.2
|
1.0
|
N
|
A:TRP275
|
3.6
|
49.8
|
1.0
|
NH1
|
A:ARG284
|
3.9
|
47.9
|
1.0
|
CA
|
A:PHE274
|
4.0
|
52.4
|
1.0
|
O
|
A:TRP275
|
4.0
|
53.2
|
1.0
|
C4
|
A:ZF7901
|
4.1
|
40.3
|
1.0
|
C2
|
A:ZF7901
|
4.1
|
37.2
|
1.0
|
C
|
A:PHE274
|
4.3
|
47.7
|
1.0
|
CD2
|
A:TYR306
|
4.5
|
68.1
|
1.0
|
CA
|
A:TRP275
|
4.5
|
52.4
|
1.0
|
CB
|
A:PHE274
|
4.5
|
53.0
|
1.0
|
C3
|
A:ZF7901
|
4.6
|
51.4
|
1.0
|
CD1
|
A:PHE274
|
4.6
|
49.0
|
1.0
|
CB
|
A:TRP275
|
4.6
|
59.4
|
1.0
|
CB
|
A:TYR306
|
4.6
|
41.5
|
1.0
|
O
|
A:PHE273
|
4.6
|
56.9
|
1.0
|
C
|
A:TRP275
|
4.7
|
52.2
|
1.0
|
|
Zinc binding site 6 out
of 7 in 7mfh
Go back to
Zinc Binding Sites List in 7mfh
Zinc binding site 6 out
of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin
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 Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn921
b:63.9
occ:1.00
|
O
|
A:HOH1148
|
2.0
|
58.9
|
1.0
|
NH2
|
A:ARG393
|
3.1
|
49.1
|
1.0
|
C
|
A:MET232
|
3.6
|
54.0
|
1.0
|
O
|
A:MET232
|
3.8
|
53.0
|
1.0
|
N
|
A:TYR233
|
3.9
|
50.4
|
1.0
|
CB
|
A:TYR233
|
3.9
|
45.1
|
1.0
|
N
|
A:MET232
|
4.0
|
46.6
|
1.0
|
CA
|
A:MET232
|
4.0
|
55.4
|
1.0
|
CG2
|
A:VAL385
|
4.2
|
44.2
|
1.0
|
CZ
|
A:ARG393
|
4.3
|
41.6
|
1.0
|
CA
|
A:TYR233
|
4.4
|
41.7
|
1.0
|
C
|
A:SER231
|
4.5
|
51.0
|
1.0
|
CG2
|
A:THR240
|
4.6
|
108.7
|
1.0
|
CE1
|
A:HIS242
|
4.7
|
65.6
|
1.0
|
NH1
|
A:ARG393
|
4.7
|
43.5
|
1.0
|
CB
|
A:THR240
|
4.7
|
107.7
|
1.0
|
CB
|
A:SER231
|
4.8
|
37.1
|
1.0
|
O
|
A:HOH1049
|
4.9
|
36.4
|
1.0
|
NE2
|
A:HIS242
|
5.0
|
74.0
|
1.0
|
O
|
A:SER231
|
5.0
|
50.6
|
1.0
|
|
Zinc binding site 7 out
of 7 in 7mfh
Go back to
Zinc Binding Sites List in 7mfh
Zinc binding site 7 out
of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn922
b:27.9
occ:1.00
|
NZ
|
A:LYS208
|
3.4
|
70.7
|
1.0
|
N
|
A:ASN230
|
3.5
|
44.5
|
1.0
|
NH1
|
A:ARG391
|
3.7
|
45.7
|
1.0
|
CD2
|
A:LEU389
|
3.8
|
61.3
|
1.0
|
N
|
A:SER231
|
3.8
|
43.0
|
1.0
|
CA
|
A:GLY229
|
3.9
|
49.2
|
1.0
|
O
|
A:SER231
|
4.1
|
50.6
|
1.0
|
CG
|
A:LYS208
|
4.1
|
55.0
|
1.0
|
CG1
|
A:VAL385
|
4.1
|
36.3
|
1.0
|
C
|
A:GLY229
|
4.2
|
60.0
|
1.0
|
CD1
|
A:LEU389
|
4.2
|
52.2
|
1.0
|
CE
|
A:LYS208
|
4.3
|
78.8
|
1.0
|
CA
|
A:ASN230
|
4.4
|
47.1
|
1.0
|
CG
|
A:LEU389
|
4.5
|
45.5
|
1.0
|
CB
|
A:ASN230
|
4.5
|
46.9
|
1.0
|
C
|
A:ASN230
|
4.6
|
44.5
|
1.0
|
CA
|
A:SER231
|
4.7
|
46.5
|
1.0
|
CB
|
A:SER231
|
4.7
|
37.1
|
1.0
|
CD
|
A:LYS208
|
4.8
|
56.3
|
1.0
|
C
|
A:SER231
|
4.9
|
51.0
|
1.0
|
CZ
|
A:ARG391
|
4.9
|
44.4
|
1.0
|
|
Reference:
B.Ma,
L.Zhang,
L.Sun,
Z.Xin,
G.Kumaravel,
D.Marcotte,
J.V.Chodaparambil,
Q.Wang,
A.Wehr,
J.Jing,
V.S.Hong,
T.Wang,
C.Huang,
Z.Shao,
S.Mi.
Discovery of Potent Selective Nonzinc Binding Autotaxin Inhibitor Bio-32546. Acs Med.Chem.Lett. V. 12 1124 2021.
ISSN: ISSN 1948-5875
PubMed: 34267882
DOI: 10.1021/ACSMEDCHEMLETT.1C00211
Page generated: Tue Oct 29 23:18:05 2024
|