Calcium in PDB 6ela: Crystal Structure of MMP12 in Complex with Inhibitor BE4.
Enzymatic activity of Crystal Structure of MMP12 in Complex with Inhibitor BE4.
All present enzymatic activity of Crystal Structure of MMP12 in Complex with Inhibitor BE4.:
3.4.24.65;
Protein crystallography data
The structure of Crystal Structure of MMP12 in Complex with Inhibitor BE4., PDB code: 6ela
was solved by
L.Ciccone,
L.Tepshi,
E.Nuti,
A.Rossello,
E.A.Stura,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
38.04 /
1.49
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.190,
63.320,
78.320,
90.00,
103.73,
90.00
|
|
R / Rfree (%)
|
17.1 /
20.7
|
Other elements in 6ela:
The structure of Crystal Structure of MMP12 in Complex with Inhibitor BE4. also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
(pdb code 6ela). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Crystal Structure of MMP12 in Complex with Inhibitor BE4., PDB code: 6ela:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 1 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:13.7
occ:1.00
|
O
|
A:GLY192
|
2.3
|
12.6
|
1.0
|
|
O
|
A:HOH411
|
2.3
|
20.9
|
1.0
|
|
O
|
A:GLY190
|
2.3
|
13.6
|
1.0
|
|
O
|
A:ASP158
|
2.3
|
15.1
|
1.0
|
|
O
|
A:HOH453
|
2.4
|
16.8
|
1.0
|
|
OD1
|
A:ASP194
|
2.4
|
12.7
|
1.0
|
|
CG
|
A:ASP194
|
3.4
|
12.9
|
1.0
|
|
C
|
A:GLY192
|
3.5
|
12.0
|
1.0
|
|
C
|
A:ASP158
|
3.5
|
14.6
|
1.0
|
|
C
|
A:GLY190
|
3.6
|
15.2
|
1.0
|
|
OD2
|
A:ASP194
|
3.8
|
13.5
|
1.0
|
|
C
|
A:ILE191
|
3.9
|
13.2
|
1.0
|
|
N
|
A:GLY192
|
4.0
|
15.0
|
1.0
|
|
O
|
A:ILE191
|
4.1
|
13.4
|
1.0
|
|
O
|
A:ALA157
|
4.2
|
15.7
|
1.0
|
|
N
|
A:ASP194
|
4.2
|
11.6
|
1.0
|
|
O
|
A:HOH418
|
4.3
|
25.3
|
1.0
|
|
CA
|
A:GLY192
|
4.3
|
14.4
|
1.0
|
|
CA
|
A:ASP158
|
4.3
|
13.7
|
1.0
|
|
O
|
A:GLY188
|
4.3
|
19.8
|
1.0
|
|
CA
|
A:ILE191
|
4.3
|
15.1
|
1.0
|
|
N
|
A:ILE191
|
4.4
|
16.3
|
1.0
|
|
N
|
A:ILE159
|
4.4
|
12.0
|
1.0
|
|
N
|
A:GLY193
|
4.5
|
12.2
|
1.0
|
|
N
|
A:GLY190
|
4.5
|
19.0
|
1.0
|
|
CA
|
A:GLY190
|
4.6
|
17.4
|
1.0
|
|
CB
|
A:ASP194
|
4.6
|
11.2
|
1.0
|
|
CA
|
A:ILE159
|
4.6
|
11.7
|
1.0
|
|
CA
|
A:GLY193
|
4.6
|
10.9
|
1.0
|
|
C
|
A:GLY193
|
4.7
|
12.4
|
1.0
|
|
N
|
A:LEU160
|
4.7
|
10.4
|
1.0
|
|
O
|
A:HOH432
|
4.8
|
19.8
|
1.0
|
|
CA
|
A:ASP194
|
4.8
|
12.4
|
1.0
|
|
C
|
A:SER189
|
4.8
|
19.6
|
1.0
|
|
CH2
|
A:TRP109
|
4.9
|
15.9
|
1.0
|
|
Calcium binding site 2 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 2 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:12.3
occ:1.00
|
O
|
A:GLU199
|
2.3
|
10.9
|
1.0
|
|
OE2
|
A:GLU199
|
2.4
|
11.3
|
1.0
|
|
OD2
|
A:ASP124
|
2.4
|
11.5
|
1.0
|
|
O
|
A:GLU201
|
2.4
|
11.9
|
1.0
|
|
O
|
A:HOH535
|
2.4
|
16.1
|
1.0
|
|
O
|
A:HOH548
|
2.5
|
18.1
|
1.0
|
|
OD1
|
A:ASP124
|
2.6
|
12.2
|
1.0
|
|
CG
|
A:ASP124
|
2.9
|
13.2
|
1.0
|
|
C
|
A:GLU199
|
3.4
|
10.4
|
1.0
|
|
CD
|
A:GLU199
|
3.4
|
12.4
|
1.0
|
|
C
|
A:GLU201
|
3.6
|
12.0
|
1.0
|
|
CG
|
A:GLU199
|
3.8
|
10.3
|
1.0
|
|
CA
|
A:GLU199
|
4.0
|
9.7
|
1.0
|
|
OG1
|
A:THR122
|
4.1
|
12.9
|
1.0
|
|
O
|
C:HOH577
|
4.2
|
31.1
|
1.0
|
|
CA
|
A:PHE202
|
4.3
|
12.3
|
1.0
|
|
CD1
|
A:TRP203
|
4.3
|
10.7
|
1.0
|
|
N
|
A:PHE202
|
4.4
|
10.5
|
1.0
|
|
CB
|
A:ASP124
|
4.4
|
13.1
|
1.0
|
|
N
|
A:GLU201
|
4.4
|
13.1
|
1.0
|
|
NE2
|
C:HIS112
|
4.4
|
30.0
|
1.0
|
|
N
|
A:ASP200
|
4.5
|
10.9
|
1.0
|
|
C
|
A:ASP200
|
4.5
|
12.7
|
1.0
|
|
CB
|
A:GLU199
|
4.5
|
10.9
|
1.0
|
|
OE1
|
A:GLU199
|
4.6
|
13.7
|
1.0
|
|
O
|
A:HOH478
|
4.6
|
23.2
|
1.0
|
|
CA
|
A:ASP200
|
4.6
|
12.4
|
1.0
|
|
CA
|
A:GLU201
|
4.7
|
12.2
|
1.0
|
|
CE1
|
C:HIS112
|
4.7
|
31.3
|
1.0
|
|
NH1
|
A:ARG165
|
4.7
|
23.9
|
1.0
|
|
NE1
|
A:TRP203
|
4.8
|
11.2
|
1.0
|
|
N
|
A:TRP203
|
4.8
|
9.6
|
1.0
|
|
O
|
A:ASP200
|
5.0
|
14.0
|
1.0
|
|
Calcium binding site 3 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 3 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca305
b:12.1
occ:1.00
|
O
|
A:GLY176
|
2.3
|
14.0
|
1.0
|
|
OE2
|
A:GLU201
|
2.3
|
13.1
|
1.0
|
|
OD2
|
A:ASP198
|
2.3
|
12.0
|
1.0
|
|
O
|
A:ILE180
|
2.3
|
11.6
|
1.0
|
|
OD1
|
A:ASP175
|
2.3
|
12.5
|
1.0
|
|
O
|
A:GLY178
|
2.3
|
14.8
|
1.0
|
|
CG
|
A:ASP198
|
3.4
|
12.1
|
1.0
|
|
C
|
A:ILE180
|
3.4
|
11.1
|
1.0
|
|
CG
|
A:ASP175
|
3.5
|
13.8
|
1.0
|
|
C
|
A:GLY176
|
3.5
|
14.6
|
1.0
|
|
CD
|
A:GLU201
|
3.5
|
12.1
|
1.0
|
|
C
|
A:GLY178
|
3.5
|
15.0
|
1.0
|
|
N
|
A:GLY178
|
3.9
|
13.8
|
1.0
|
|
N
|
A:ILE180
|
4.0
|
13.7
|
1.0
|
|
CB
|
A:ASP198
|
4.1
|
12.2
|
1.0
|
|
OD2
|
A:ASP175
|
4.1
|
14.6
|
1.0
|
|
C
|
A:LYS177
|
4.1
|
14.9
|
1.0
|
|
N
|
A:GLY176
|
4.1
|
15.2
|
1.0
|
|
CA
|
A:ILE180
|
4.2
|
12.6
|
1.0
|
|
OE1
|
A:GLU201
|
4.2
|
14.5
|
1.0
|
|
C
|
A:ASP175
|
4.3
|
15.7
|
1.0
|
|
N
|
A:ASP175
|
4.3
|
11.7
|
1.0
|
|
CA
|
A:GLY178
|
4.3
|
13.9
|
1.0
|
|
C
|
A:GLY179
|
4.3
|
14.4
|
1.0
|
|
CA
|
A:LYS177
|
4.3
|
15.1
|
1.0
|
|
OD1
|
A:ASP198
|
4.4
|
11.3
|
1.0
|
|
N
|
A:LEU181
|
4.4
|
10.0
|
1.0
|
|
N
|
A:LYS177
|
4.4
|
14.6
|
1.0
|
|
CA
|
A:GLY176
|
4.4
|
14.7
|
1.0
|
|
CA
|
A:LEU181
|
4.4
|
10.6
|
1.0
|
|
CG
|
A:GLU201
|
4.5
|
11.2
|
1.0
|
|
N
|
A:GLY179
|
4.5
|
14.6
|
1.0
|
|
CA
|
A:ASP175
|
4.6
|
13.5
|
1.0
|
|
CB
|
A:ASP175
|
4.7
|
13.8
|
1.0
|
|
O
|
A:LYS177
|
4.7
|
15.5
|
1.0
|
|
CA
|
A:GLY179
|
4.7
|
14.2
|
1.0
|
|
CB
|
A:ILE180
|
4.7
|
13.5
|
1.0
|
|
O
|
A:ASP175
|
4.7
|
16.3
|
1.0
|
|
O
|
A:GLY179
|
4.9
|
15.4
|
1.0
|
|
CD2
|
A:LEU181
|
5.0
|
14.8
|
1.0
|
|
Calcium binding site 4 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 4 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca303
b:16.8
occ:1.00
|
O
|
B:GLY190
|
2.3
|
17.1
|
1.0
|
|
O
|
B:GLY192
|
2.3
|
17.3
|
1.0
|
|
O
|
B:ASP158
|
2.3
|
16.6
|
1.0
|
|
O
|
B:HOH428
|
2.3
|
23.5
|
1.0
|
|
O
|
B:HOH467
|
2.4
|
19.8
|
1.0
|
|
OD1
|
B:ASP194
|
2.5
|
13.3
|
1.0
|
|
CG
|
B:ASP194
|
3.4
|
14.2
|
1.0
|
|
C
|
B:GLY190
|
3.5
|
17.1
|
1.0
|
|
C
|
B:GLY192
|
3.5
|
15.7
|
1.0
|
|
C
|
B:ASP158
|
3.5
|
15.4
|
1.0
|
|
OD2
|
B:ASP194
|
3.8
|
15.2
|
1.0
|
|
C
|
B:ILE191
|
4.0
|
16.2
|
1.0
|
|
N
|
B:GLY192
|
4.0
|
15.3
|
1.0
|
|
O
|
B:HOH413
|
4.1
|
28.0
|
1.0
|
|
O
|
B:ALA157
|
4.2
|
21.2
|
1.0
|
|
N
|
B:ASP194
|
4.2
|
14.7
|
1.0
|
|
O
|
B:ILE191
|
4.2
|
16.1
|
1.0
|
|
CA
|
B:GLY192
|
4.3
|
15.4
|
1.0
|
|
CA
|
B:ASP158
|
4.3
|
17.1
|
1.0
|
|
CA
|
B:GLY190
|
4.4
|
19.4
|
1.0
|
|
O
|
B:GLY188
|
4.4
|
21.0
|
1.0
|
|
N
|
B:GLY190
|
4.4
|
19.9
|
1.0
|
|
N
|
B:ILE191
|
4.4
|
17.4
|
1.0
|
|
CA
|
B:ILE191
|
4.4
|
17.0
|
1.0
|
|
N
|
B:GLY193
|
4.5
|
14.8
|
1.0
|
|
N
|
B:ILE159
|
4.5
|
14.6
|
1.0
|
|
CA
|
B:GLY193
|
4.5
|
14.2
|
1.0
|
|
CB
|
B:ASP194
|
4.6
|
14.8
|
1.0
|
|
C
|
B:GLY193
|
4.6
|
14.9
|
1.0
|
|
CA
|
B:ILE159
|
4.6
|
13.7
|
1.0
|
|
N
|
B:LEU160
|
4.7
|
14.4
|
1.0
|
|
O
|
B:HOH446
|
4.8
|
23.9
|
1.0
|
|
CA
|
B:ASP194
|
4.8
|
14.2
|
1.0
|
|
C
|
B:SER189
|
4.8
|
20.8
|
1.0
|
|
CH2
|
B:TRP109
|
4.9
|
18.8
|
1.0
|
|
Calcium binding site 5 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 5 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca304
b:17.0
occ:1.00
|
O
|
B:GLU199
|
2.3
|
15.6
|
1.0
|
|
O
|
B:HOH525
|
2.4
|
18.9
|
1.0
|
|
OD2
|
B:ASP124
|
2.4
|
18.2
|
1.0
|
|
O
|
B:HOH534
|
2.4
|
17.9
|
1.0
|
|
OE2
|
B:GLU199
|
2.4
|
16.2
|
1.0
|
|
O
|
B:GLU201
|
2.4
|
15.9
|
1.0
|
|
OD1
|
B:ASP124
|
2.6
|
19.8
|
1.0
|
|
CG
|
B:ASP124
|
2.8
|
18.8
|
1.0
|
|
C
|
B:GLU199
|
3.5
|
15.1
|
1.0
|
|
CD
|
B:GLU199
|
3.5
|
17.1
|
1.0
|
|
C
|
B:GLU201
|
3.6
|
16.0
|
1.0
|
|
CG
|
B:GLU199
|
3.8
|
15.7
|
1.0
|
|
CA
|
B:GLU199
|
4.1
|
14.5
|
1.0
|
|
OG1
|
B:THR122
|
4.2
|
16.5
|
1.0
|
|
CA
|
B:PHE202
|
4.2
|
16.9
|
1.0
|
|
CB
|
B:ASP124
|
4.3
|
17.9
|
1.0
|
|
N
|
B:PHE202
|
4.3
|
16.2
|
1.0
|
|
CD1
|
B:TRP203
|
4.4
|
13.1
|
1.0
|
|
N
|
B:GLU201
|
4.5
|
14.5
|
1.0
|
|
N
|
B:ASP200
|
4.5
|
15.0
|
1.0
|
|
C
|
B:ASP200
|
4.5
|
15.1
|
1.0
|
|
CB
|
B:GLU199
|
4.6
|
15.9
|
1.0
|
|
O
|
B:HOH569
|
4.6
|
35.0
|
1.0
|
|
O
|
B:HOH483
|
4.6
|
28.1
|
1.0
|
|
OE1
|
B:GLU199
|
4.6
|
17.6
|
1.0
|
|
O
|
B:HOH435
|
4.6
|
30.1
|
1.0
|
|
CA
|
B:ASP200
|
4.7
|
14.8
|
1.0
|
|
CA
|
B:GLU201
|
4.7
|
14.6
|
1.0
|
|
NH1
|
B:ARG165
|
4.7
|
28.2
|
1.0
|
|
N
|
B:TRP203
|
4.8
|
16.3
|
1.0
|
|
CD1
|
B:PHE202
|
4.8
|
23.0
|
1.0
|
|
NE1
|
B:TRP203
|
4.9
|
13.1
|
1.0
|
|
O
|
B:HOH535
|
4.9
|
30.2
|
1.0
|
|
Calcium binding site 6 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 6 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca305
b:14.9
occ:1.00
|
O
|
B:GLY176
|
2.3
|
15.5
|
1.0
|
|
O
|
B:ILE180
|
2.3
|
13.8
|
1.0
|
|
OE2
|
B:GLU201
|
2.3
|
13.1
|
1.0
|
|
OD2
|
B:ASP198
|
2.3
|
12.6
|
1.0
|
|
O
|
B:GLY178
|
2.3
|
16.0
|
1.0
|
|
OD1
|
B:ASP175
|
2.3
|
14.2
|
1.0
|
|
CG
|
B:ASP198
|
3.4
|
12.8
|
1.0
|
|
C
|
B:ILE180
|
3.4
|
11.8
|
1.0
|
|
CD
|
B:GLU201
|
3.5
|
13.6
|
1.0
|
|
C
|
B:GLY176
|
3.5
|
16.6
|
1.0
|
|
CG
|
B:ASP175
|
3.5
|
14.8
|
1.0
|
|
C
|
B:GLY178
|
3.5
|
16.3
|
1.0
|
|
N
|
B:GLY178
|
3.9
|
15.4
|
1.0
|
|
N
|
B:ILE180
|
4.0
|
14.0
|
1.0
|
|
CB
|
B:ASP198
|
4.0
|
12.5
|
1.0
|
|
OD2
|
B:ASP175
|
4.1
|
15.8
|
1.0
|
|
N
|
B:GLY176
|
4.1
|
14.0
|
1.0
|
|
OE1
|
B:GLU201
|
4.1
|
14.7
|
1.0
|
|
C
|
B:LYS177
|
4.1
|
16.7
|
1.0
|
|
CA
|
B:ILE180
|
4.2
|
12.0
|
1.0
|
|
C
|
B:ASP175
|
4.2
|
13.9
|
1.0
|
|
C
|
B:GLY179
|
4.3
|
14.6
|
1.0
|
|
CA
|
B:GLY178
|
4.3
|
15.0
|
1.0
|
|
OD1
|
B:ASP198
|
4.3
|
14.0
|
1.0
|
|
N
|
B:ASP175
|
4.3
|
13.3
|
1.0
|
|
N
|
B:LEU181
|
4.3
|
10.9
|
1.0
|
|
CA
|
B:LYS177
|
4.4
|
17.5
|
1.0
|
|
N
|
B:LYS177
|
4.4
|
17.0
|
1.0
|
|
CA
|
B:GLY176
|
4.4
|
15.5
|
1.0
|
|
CA
|
B:LEU181
|
4.4
|
12.5
|
1.0
|
|
O
|
B:HOH482
|
4.5
|
24.1
|
1.0
|
|
N
|
B:GLY179
|
4.6
|
17.1
|
1.0
|
|
CG
|
B:GLU201
|
4.6
|
12.7
|
1.0
|
|
CA
|
B:ASP175
|
4.6
|
13.5
|
1.0
|
|
O
|
B:ASP175
|
4.6
|
15.6
|
1.0
|
|
CB
|
B:ASP175
|
4.7
|
13.4
|
1.0
|
|
CA
|
B:GLY179
|
4.7
|
16.1
|
1.0
|
|
O
|
B:LYS177
|
4.7
|
17.9
|
1.0
|
|
CB
|
B:ILE180
|
4.7
|
12.0
|
1.0
|
|
O
|
B:GLY179
|
4.8
|
14.5
|
1.0
|
|
CD2
|
B:LEU181
|
5.0
|
13.0
|
1.0
|
|
O
|
B:HOH433
|
5.0
|
15.2
|
1.0
|
|
Calcium binding site 7 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 7 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca303
b:14.7
occ:1.00
|
O
|
C:ASP158
|
2.3
|
15.3
|
1.0
|
|
O
|
C:GLY190
|
2.3
|
18.0
|
1.0
|
|
O
|
C:GLY192
|
2.3
|
13.5
|
1.0
|
|
O
|
C:HOH422
|
2.3
|
20.3
|
1.0
|
|
O
|
C:HOH489
|
2.3
|
19.7
|
1.0
|
|
OD1
|
C:ASP194
|
2.4
|
13.8
|
1.0
|
|
CG
|
C:ASP194
|
3.4
|
13.1
|
1.0
|
|
C
|
C:ASP158
|
3.5
|
13.7
|
1.0
|
|
C
|
C:GLY192
|
3.5
|
12.4
|
1.0
|
|
C
|
C:GLY190
|
3.6
|
17.6
|
1.0
|
|
OD2
|
C:ASP194
|
3.8
|
13.0
|
1.0
|
|
C
|
C:ILE191
|
4.0
|
16.1
|
1.0
|
|
O
|
C:HOH427
|
4.0
|
30.7
|
1.0
|
|
N
|
C:GLY192
|
4.1
|
16.6
|
1.0
|
|
O
|
C:ALA157
|
4.2
|
16.5
|
1.0
|
|
O
|
C:ILE191
|
4.2
|
15.6
|
1.0
|
|
N
|
C:ASP194
|
4.2
|
12.0
|
1.0
|
|
CA
|
C:ASP158
|
4.3
|
13.5
|
1.0
|
|
CA
|
C:ILE191
|
4.3
|
16.7
|
1.0
|
|
CA
|
C:GLY192
|
4.4
|
14.7
|
1.0
|
|
N
|
C:ILE191
|
4.4
|
17.2
|
1.0
|
|
O
|
C:GLY188
|
4.4
|
19.0
|
1.0
|
|
N
|
C:ILE159
|
4.4
|
11.8
|
1.0
|
|
N
|
C:GLY190
|
4.5
|
18.9
|
1.0
|
|
N
|
C:GLY193
|
4.5
|
12.2
|
1.0
|
|
CA
|
C:GLY190
|
4.5
|
18.8
|
1.0
|
|
CA
|
C:GLY193
|
4.6
|
12.2
|
1.0
|
|
CA
|
C:ILE159
|
4.6
|
11.5
|
1.0
|
|
CB
|
C:ASP194
|
4.6
|
12.3
|
1.0
|
|
C
|
C:GLY193
|
4.6
|
11.9
|
1.0
|
|
N
|
C:LEU160
|
4.6
|
11.8
|
1.0
|
|
O
|
C:HOH434
|
4.7
|
22.5
|
1.0
|
|
CA
|
C:ASP194
|
4.8
|
12.3
|
1.0
|
|
C
|
C:SER189
|
4.9
|
18.8
|
1.0
|
|
CH2
|
C:TRP109
|
4.9
|
17.1
|
1.0
|
|
Calcium binding site 8 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 8 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca304
b:12.8
occ:1.00
|
O
|
C:GLU199
|
2.3
|
12.1
|
1.0
|
|
OE2
|
C:GLU199
|
2.4
|
12.9
|
1.0
|
|
O
|
C:GLU201
|
2.4
|
12.5
|
1.0
|
|
OD2
|
C:ASP124
|
2.4
|
12.4
|
1.0
|
|
O
|
C:HOH549
|
2.4
|
15.7
|
1.0
|
|
O
|
C:HOH525
|
2.4
|
17.2
|
1.0
|
|
OD1
|
C:ASP124
|
2.7
|
13.6
|
1.0
|
|
CG
|
C:ASP124
|
2.9
|
12.4
|
1.0
|
|
CD
|
C:GLU199
|
3.4
|
14.6
|
1.0
|
|
C
|
C:GLU199
|
3.4
|
12.7
|
1.0
|
|
C
|
C:GLU201
|
3.6
|
13.0
|
1.0
|
|
CG
|
C:GLU199
|
3.8
|
12.4
|
1.0
|
|
CA
|
C:GLU199
|
4.1
|
11.7
|
1.0
|
|
OG1
|
C:THR122
|
4.1
|
13.4
|
1.0
|
|
CA
|
C:PHE202
|
4.2
|
13.2
|
1.0
|
|
N
|
C:PHE202
|
4.3
|
12.1
|
1.0
|
|
CD1
|
C:TRP203
|
4.3
|
10.4
|
1.0
|
|
CB
|
C:ASP124
|
4.4
|
13.3
|
1.0
|
|
O
|
C:HOH491
|
4.4
|
32.0
|
1.0
|
|
N
|
C:GLU201
|
4.4
|
11.6
|
1.0
|
|
N
|
C:ASP200
|
4.5
|
12.0
|
1.0
|
|
C
|
C:ASP200
|
4.5
|
12.8
|
1.0
|
|
OE1
|
C:GLU199
|
4.5
|
14.7
|
1.0
|
|
CB
|
C:GLU199
|
4.6
|
12.8
|
1.0
|
|
CA
|
C:ASP200
|
4.6
|
12.7
|
1.0
|
|
CA
|
C:GLU201
|
4.7
|
12.0
|
1.0
|
|
O
|
C:HOH519
|
4.7
|
26.8
|
1.0
|
|
NH1
|
C:ARG165
|
4.7
|
20.4
|
1.0
|
|
N
|
C:TRP203
|
4.8
|
11.5
|
1.0
|
|
NE1
|
C:TRP203
|
4.8
|
11.1
|
1.0
|
|
O
|
C:HOH530
|
4.9
|
33.2
|
1.0
|
|
Calcium binding site 9 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 9 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca305
b:13.7
occ:1.00
|
O
|
C:GLY176
|
2.3
|
16.5
|
1.0
|
|
OD2
|
C:ASP198
|
2.3
|
13.4
|
1.0
|
|
OD1
|
C:ASP175
|
2.3
|
14.7
|
1.0
|
|
O
|
C:GLY178
|
2.3
|
14.9
|
1.0
|
|
OE2
|
C:GLU201
|
2.3
|
14.0
|
1.0
|
|
O
|
C:ILE180
|
2.3
|
13.8
|
1.0
|
|
CG
|
C:ASP198
|
3.4
|
12.4
|
1.0
|
|
C
|
C:ILE180
|
3.4
|
10.8
|
1.0
|
|
CG
|
C:ASP175
|
3.5
|
15.0
|
1.0
|
|
C
|
C:GLY176
|
3.5
|
15.3
|
1.0
|
|
C
|
C:GLY178
|
3.5
|
15.9
|
1.0
|
|
CD
|
C:GLU201
|
3.5
|
13.6
|
1.0
|
|
N
|
C:GLY178
|
3.8
|
15.2
|
1.0
|
|
N
|
C:ILE180
|
4.0
|
12.9
|
1.0
|
|
CB
|
C:ASP198
|
4.0
|
12.0
|
1.0
|
|
OD2
|
C:ASP175
|
4.0
|
15.8
|
1.0
|
|
N
|
C:GLY176
|
4.1
|
15.2
|
1.0
|
|
C
|
C:LYS177
|
4.1
|
15.8
|
1.0
|
|
OE1
|
C:GLU201
|
4.2
|
16.8
|
1.0
|
|
CA
|
C:ILE180
|
4.2
|
12.2
|
1.0
|
|
CA
|
C:GLY178
|
4.3
|
15.4
|
1.0
|
|
C
|
C:ASP175
|
4.3
|
15.7
|
1.0
|
|
OD1
|
C:ASP198
|
4.3
|
11.5
|
1.0
|
|
N
|
C:ASP175
|
4.3
|
13.3
|
1.0
|
|
C
|
C:GLY179
|
4.3
|
14.7
|
1.0
|
|
CA
|
C:LYS177
|
4.4
|
16.4
|
1.0
|
|
N
|
C:LEU181
|
4.4
|
11.3
|
1.0
|
|
N
|
C:LYS177
|
4.4
|
15.8
|
1.0
|
|
CA
|
C:GLY176
|
4.4
|
16.2
|
1.0
|
|
CA
|
C:LEU181
|
4.5
|
11.1
|
1.0
|
|
N
|
C:GLY179
|
4.5
|
15.8
|
1.0
|
|
CG
|
C:GLU201
|
4.6
|
11.8
|
1.0
|
|
CA
|
C:ASP175
|
4.6
|
14.2
|
1.0
|
|
CB
|
C:ASP175
|
4.6
|
15.9
|
1.0
|
|
O
|
C:LYS177
|
4.7
|
17.1
|
1.0
|
|
CA
|
C:GLY179
|
4.7
|
13.9
|
1.0
|
|
CB
|
C:ILE180
|
4.7
|
12.8
|
1.0
|
|
O
|
C:ASP175
|
4.8
|
17.0
|
1.0
|
|
O
|
C:GLY179
|
4.9
|
13.6
|
1.0
|
|
CD2
|
C:LEU181
|
4.9
|
15.2
|
1.0
|
|
O
|
C:HOH440
|
5.0
|
14.6
|
1.0
|
|
Calcium binding site 10 out
of 12 in 6ela
Go back to
Calcium Binding Sites List in 6ela
Calcium binding site 10 out
of 12 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca303
b:15.6
occ:1.00
|
O
|
D:GLY192
|
2.3
|
16.0
|
1.0
|
|
O
|
D:GLY190
|
2.3
|
16.9
|
1.0
|
|
O
|
D:ASP158
|
2.3
|
14.9
|
1.0
|
|
O
|
D:HOH450
|
2.3
|
16.6
|
1.0
|
|
O
|
D:HOH406
|
2.4
|
25.0
|
1.0
|
|
OD1
|
D:ASP194
|
2.4
|
13.5
|
1.0
|
|
CG
|
D:ASP194
|
3.4
|
13.5
|
1.0
|
|
C
|
D:GLY192
|
3.5
|
14.6
|
1.0
|
|
C
|
D:ASP158
|
3.5
|
14.7
|
1.0
|
|
C
|
D:GLY190
|
3.5
|
16.9
|
1.0
|
|
O
|
D:HOH437
|
3.7
|
19.1
|
0.4
|
|
OD2
|
D:ASP194
|
3.8
|
14.3
|
1.0
|
|
O
|
D:HOH554
|
3.9
|
35.4
|
1.0
|
|
C
|
D:ILE191
|
4.0
|
15.4
|
1.0
|
|
N
|
D:GLY192
|
4.1
|
15.3
|
1.0
|
|
O
|
D:ALA157
|
4.2
|
17.4
|
1.0
|
|
O
|
D:ILE191
|
4.2
|
14.5
|
1.0
|
|
N
|
D:ASP194
|
4.2
|
13.3
|
1.0
|
|
O
|
D:GLY188
|
4.3
|
19.4
|
1.0
|
|
CA
|
D:GLY192
|
4.3
|
14.5
|
1.0
|
|
CA
|
D:ASP158
|
4.3
|
15.0
|
1.0
|
|
N
|
D:GLY190
|
4.4
|
18.2
|
1.0
|
|
N
|
D:ILE159
|
4.4
|
13.4
|
1.0
|
|
CA
|
D:GLY190
|
4.4
|
18.1
|
1.0
|
|
N
|
D:GLY193
|
4.4
|
13.9
|
1.0
|
|
N
|
D:ILE191
|
4.4
|
17.3
|
1.0
|
|
CA
|
D:ILE191
|
4.5
|
16.8
|
1.0
|
|
CA
|
D:GLY193
|
4.5
|
13.0
|
1.0
|
|
CA
|
D:ILE159
|
4.6
|
12.9
|
1.0
|
|
N
|
D:LEU160
|
4.6
|
13.2
|
1.0
|
|
C
|
D:GLY193
|
4.6
|
13.6
|
1.0
|
|
CB
|
D:ASP194
|
4.6
|
12.5
|
1.0
|
|
O
|
D:HOH437
|
4.6
|
17.0
|
0.6
|
|
CA
|
D:ASP194
|
4.8
|
12.4
|
1.0
|
|
C
|
D:SER189
|
4.8
|
20.5
|
1.0
|
|
CH2
|
D:TRP109
|
4.8
|
18.0
|
1.0
|
|
O
|
D:HOH439
|
4.9
|
22.1
|
1.0
|
|
Reference:
E.Nuti,
D.Cuffaro,
E.Bernardini,
C.Camodeca,
L.Panelli,
S.Chaves,
L.Ciccone,
L.Tepshi,
L.Vera,
E.Orlandini,
S.Nencetti,
E.A.Stura,
M.A.Santos,
V.Dive,
A.Rossello.
Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, uc(Nmr), and Crystallographic Studies. J. Med. Chem. V. 61 4421 2018.
ISSN: ISSN 1520-4804
PubMed: 29727184
DOI: 10.1021/ACS.JMEDCHEM.8B00096
Page generated: Mon Jul 15 18:26:39 2024
|
