Calcium in PDB 7ovy: Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain
Enzymatic activity of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain
All present enzymatic activity of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain:
3.4.24.65;
Protein crystallography data
The structure of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain, PDB code: 7ovy
was solved by
L.Ciccone,
A.Rossello,
L.Vera,
E.Nuti,
E.A.Stura,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.89 /
1.24
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.34,
60.45,
54.05,
90,
115.24,
90
|
R / Rfree (%)
|
18.4 /
20.9
|
Other elements in 7ovy:
The structure of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain
(pdb code 7ovy). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain, PDB code: 7ovy:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 7ovy
Go back to
Calcium Binding Sites List in 7ovy
Calcium binding site 1 out
of 3 in the Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:12.8
occ:1.00
|
O
|
A:GLY192
|
2.3
|
10.6
|
1.0
|
O
|
A:ASP158
|
2.3
|
13.6
|
1.0
|
O
|
A:GLY190
|
2.3
|
16.1
|
1.0
|
O
|
A:HOH425
|
2.4
|
19.0
|
1.0
|
O
|
A:HOH464
|
2.4
|
13.3
|
1.0
|
OD1
|
A:ASP194
|
2.4
|
11.2
|
1.0
|
CG
|
A:ASP194
|
3.4
|
10.1
|
1.0
|
C
|
A:ASP158
|
3.4
|
12.2
|
1.0
|
C
|
A:GLY192
|
3.5
|
10.6
|
1.0
|
C
|
A:GLY190
|
3.6
|
16.4
|
1.0
|
OD2
|
A:ASP194
|
3.8
|
12.8
|
1.0
|
O
|
A:HOH495
|
4.0
|
26.2
|
1.0
|
C
|
A:ILE191
|
4.0
|
13.0
|
1.0
|
N
|
A:GLY192
|
4.1
|
11.1
|
1.0
|
O
|
A:ALA157
|
4.1
|
17.5
|
1.0
|
O
|
A:ILE191
|
4.2
|
12.4
|
1.0
|
CA
|
A:ASP158
|
4.2
|
11.6
|
1.0
|
N
|
A:ASP194
|
4.3
|
9.7
|
1.0
|
CA
|
A:GLY192
|
4.4
|
12.0
|
1.0
|
N
|
A:ILE159
|
4.4
|
10.7
|
1.0
|
CA
|
A:ILE191
|
4.4
|
15.3
|
1.0
|
N
|
A:ILE191
|
4.4
|
15.7
|
1.0
|
O
|
A:GLY188
|
4.4
|
16.0
|
1.0
|
N
|
A:GLY193
|
4.4
|
9.9
|
1.0
|
CA
|
A:GLY190
|
4.5
|
21.7
|
1.0
|
CA
|
A:ILE159
|
4.5
|
9.7
|
1.0
|
CA
|
A:GLY193
|
4.5
|
11.2
|
1.0
|
N
|
A:GLY190
|
4.5
|
19.3
|
1.0
|
N
|
A:LEU160
|
4.6
|
11.2
|
1.0
|
CB
|
A:ASP194
|
4.6
|
10.4
|
1.0
|
C
|
A:GLY193
|
4.7
|
9.4
|
1.0
|
O
|
A:HOH458
|
4.8
|
15.9
|
1.0
|
CA
|
A:ASP194
|
4.8
|
8.8
|
1.0
|
C
|
A:SER189
|
4.8
|
16.9
|
0.7
|
C
|
A:SER189
|
4.9
|
17.1
|
0.3
|
|
Calcium binding site 2 out
of 3 in 7ovy
Go back to
Calcium Binding Sites List in 7ovy
Calcium binding site 2 out
of 3 in the Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:9.5
occ:1.00
|
O
|
A:GLU199
|
2.3
|
9.9
|
1.0
|
O
|
A:HOH570
|
2.4
|
13.5
|
1.0
|
O
|
A:HOH533
|
2.4
|
15.2
|
1.0
|
O
|
A:GLU201
|
2.4
|
10.0
|
1.0
|
OE2
|
A:GLU199
|
2.4
|
8.1
|
1.0
|
OD2
|
A:ASP124
|
2.4
|
8.9
|
1.0
|
OD1
|
A:ASP124
|
2.6
|
10.5
|
1.0
|
CG
|
A:ASP124
|
2.9
|
10.6
|
1.0
|
C
|
A:GLU199
|
3.4
|
10.2
|
1.0
|
CD
|
A:GLU199
|
3.5
|
9.1
|
1.0
|
C
|
A:GLU201
|
3.6
|
9.1
|
1.0
|
CG
|
A:GLU199
|
3.9
|
9.6
|
1.0
|
CA
|
A:GLU199
|
4.1
|
7.8
|
1.0
|
OG1
|
A:THR122
|
4.1
|
8.7
|
1.0
|
CA
|
A:PHE202
|
4.2
|
10.5
|
1.0
|
O
|
A:HOH620
|
4.3
|
24.5
|
1.0
|
N
|
A:PHE202
|
4.3
|
8.8
|
1.0
|
CD1
|
A:TRP203
|
4.3
|
7.5
|
1.0
|
CB
|
A:ASP124
|
4.4
|
9.4
|
1.0
|
N
|
A:GLU201
|
4.4
|
9.8
|
1.0
|
N
|
A:ASP200
|
4.5
|
9.1
|
1.0
|
C
|
A:ASP200
|
4.5
|
13.8
|
1.0
|
OE1
|
A:GLU199
|
4.6
|
11.8
|
1.0
|
CB
|
A:GLU199
|
4.6
|
9.0
|
1.0
|
NH1
|
A:ARG165
|
4.6
|
18.6
|
1.0
|
CA
|
A:ASP200
|
4.7
|
10.5
|
1.0
|
CA
|
A:GLU201
|
4.7
|
8.9
|
1.0
|
O
|
A:HOH474
|
4.8
|
17.8
|
1.0
|
N
|
A:TRP203
|
4.8
|
8.4
|
1.0
|
NE1
|
A:TRP203
|
4.8
|
9.3
|
1.0
|
CD1
|
A:PHE202
|
4.9
|
11.2
|
1.0
|
O
|
A:ASP200
|
5.0
|
14.6
|
1.0
|
|
Calcium binding site 3 out
of 3 in 7ovy
Go back to
Calcium Binding Sites List in 7ovy
Calcium binding site 3 out
of 3 in the Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca305
b:10.5
occ:1.00
|
OE2
|
A:GLU201
|
2.2
|
16.2
|
1.0
|
O
|
A:ILE180
|
2.3
|
12.3
|
1.0
|
O
|
A:GLY176
|
2.3
|
13.1
|
1.0
|
O
|
A:GLY178
|
2.3
|
13.9
|
1.0
|
OD1
|
A:ASP175
|
2.4
|
11.4
|
1.0
|
OD2
|
A:ASP198
|
2.4
|
11.0
|
1.0
|
C
|
A:ILE180
|
3.5
|
11.5
|
1.0
|
CG
|
A:ASP198
|
3.5
|
9.7
|
1.0
|
CD
|
A:GLU201
|
3.5
|
15.1
|
1.0
|
C
|
A:GLY178
|
3.5
|
15.7
|
1.0
|
CG
|
A:ASP175
|
3.5
|
14.1
|
1.0
|
C
|
A:GLY176
|
3.5
|
14.8
|
1.0
|
N
|
A:GLY178
|
3.8
|
13.4
|
1.0
|
N
|
A:ILE180
|
3.9
|
11.1
|
1.0
|
OD2
|
A:ASP175
|
4.1
|
14.7
|
1.0
|
CB
|
A:ASP198
|
4.1
|
8.3
|
1.0
|
C
|
A:LYS177
|
4.1
|
13.5
|
1.0
|
N
|
A:GLY176
|
4.1
|
11.3
|
1.0
|
CA
|
A:ILE180
|
4.2
|
10.9
|
1.0
|
OE1
|
A:GLU201
|
4.2
|
13.5
|
1.0
|
C
|
A:GLY179
|
4.2
|
12.2
|
1.0
|
CA
|
A:GLY178
|
4.3
|
15.9
|
1.0
|
N
|
A:ASP175
|
4.3
|
11.8
|
1.0
|
C
|
A:ASP175
|
4.3
|
13.8
|
1.0
|
OD1
|
A:ASP198
|
4.4
|
9.9
|
1.0
|
CA
|
A:LYS177
|
4.4
|
13.8
|
1.0
|
N
|
A:LYS177
|
4.4
|
12.8
|
1.0
|
CG
|
A:GLU201
|
4.4
|
10.9
|
1.0
|
CA
|
A:GLY176
|
4.5
|
13.9
|
1.0
|
N
|
A:LEU181
|
4.5
|
11.1
|
1.0
|
N
|
A:GLY179
|
4.5
|
15.6
|
1.0
|
CA
|
A:GLY179
|
4.7
|
16.5
|
1.0
|
CA
|
A:LEU181
|
4.7
|
9.6
|
1.0
|
CA
|
A:ASP175
|
4.7
|
12.9
|
1.0
|
CB
|
A:ASP175
|
4.7
|
14.8
|
1.0
|
O
|
A:GLY179
|
4.7
|
16.7
|
1.0
|
O
|
A:LYS177
|
4.8
|
20.5
|
1.0
|
CB
|
A:ILE180
|
4.8
|
12.1
|
1.0
|
O
|
A:ASP175
|
4.8
|
15.9
|
1.0
|
O
|
A:HOH571
|
4.9
|
28.4
|
1.0
|
|
Reference:
D.Cuffaro,
C.Camodeca,
T.Tuccinardi,
L.Ciccone,
J.W.Bartsch,
T.Kellermann,
L.Cook,
E.Nuti,
A.Rossello.
Discovery of Dimeric Arylsulfonamides As Potent ADAM8 Inhibitors Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00411
Page generated: Fri Nov 5 11:40:13 2021
|