Calcium in PDB 3kry: Crystal Structure of Mmp-13 in Complex with Sc-78080
Protein crystallography data
The structure of Crystal Structure of Mmp-13 in Complex with Sc-78080, PDB code: 3kry
was solved by
J.R.Kiefer,
J.M.Williams,
D.P.Becker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.68 /
1.90
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
36.317,
70.016,
69.094,
92.42,
94.23,
104.94
|
|
R / Rfree (%)
|
20.6 /
25.6
|
Other elements in 3kry:
The structure of Crystal Structure of Mmp-13 in Complex with Sc-78080 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Mmp-13 in Complex with Sc-78080
(pdb code 3kry). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Mmp-13 in Complex with Sc-78080, PDB code: 3kry:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 3kry
Go back to
Calcium Binding Sites List in 3kry
Calcium binding site 1 out
of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080
 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 Mmp-13 in Complex with Sc-78080 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1996
b:26.9
occ:1.00
|
O
|
A:ASP162
|
2.3
|
9.4
|
1.0
|
|
O
|
A:HOH303
|
2.3
|
23.2
|
1.0
|
|
O
|
A:GLY196
|
2.4
|
13.9
|
1.0
|
|
O
|
A:ASN194
|
2.4
|
19.3
|
1.0
|
|
OD1
|
A:ASP198
|
2.5
|
7.7
|
1.0
|
|
O
|
A:HOH14
|
2.6
|
15.7
|
1.0
|
|
C
|
A:GLY196
|
3.5
|
14.1
|
1.0
|
|
C
|
A:ASP162
|
3.5
|
10.0
|
1.0
|
|
CG
|
A:ASP198
|
3.5
|
10.2
|
1.0
|
|
C
|
A:ASN194
|
3.6
|
18.9
|
1.0
|
|
C
|
A:TYR195
|
3.8
|
16.8
|
1.0
|
|
N
|
A:GLY196
|
3.9
|
15.7
|
1.0
|
|
O
|
A:TYR195
|
4.0
|
16.4
|
1.0
|
|
OD2
|
A:ASP198
|
4.0
|
10.1
|
1.0
|
|
O
|
A:HOH23
|
4.1
|
25.9
|
1.0
|
|
N
|
A:ASP198
|
4.1
|
11.2
|
1.0
|
|
O
|
A:ALA161
|
4.2
|
11.3
|
1.0
|
|
CA
|
A:GLY196
|
4.2
|
14.8
|
1.0
|
|
CA
|
A:ASP162
|
4.3
|
10.1
|
1.0
|
|
CA
|
A:TYR195
|
4.4
|
17.9
|
1.0
|
|
N
|
A:GLY197
|
4.4
|
13.1
|
1.0
|
|
N
|
A:TYR195
|
4.4
|
18.4
|
1.0
|
|
N
|
A:ILE163
|
4.4
|
9.7
|
1.0
|
|
O
|
A:HOH7
|
4.5
|
15.0
|
1.0
|
|
O
|
A:GLY192
|
4.5
|
16.6
|
1.0
|
|
N
|
A:ASN194
|
4.6
|
18.8
|
1.0
|
|
N
|
A:MET164
|
4.6
|
10.6
|
1.0
|
|
CA
|
A:GLY197
|
4.6
|
12.3
|
1.0
|
|
CA
|
A:ASN194
|
4.6
|
19.4
|
1.0
|
|
C
|
A:GLY197
|
4.6
|
11.7
|
1.0
|
|
CA
|
A:ILE163
|
4.7
|
9.9
|
1.0
|
|
CG
|
A:MET164
|
4.7
|
10.5
|
1.0
|
|
CB
|
A:ASP198
|
4.7
|
10.4
|
1.0
|
|
CA
|
A:ASP198
|
4.8
|
10.8
|
1.0
|
|
C
|
A:PRO193
|
4.9
|
18.4
|
1.0
|
|
Calcium binding site 2 out
of 8 in 3kry
Go back to
Calcium Binding Sites List in 3kry
Calcium binding site 2 out
of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080
 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 Mmp-13 in Complex with Sc-78080 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1997
b:14.9
occ:1.00
|
OE2
|
A:GLU205
|
2.1
|
11.2
|
1.0
|
|
O
|
A:GLY180
|
2.2
|
10.1
|
1.0
|
|
O
|
A:SER182
|
2.3
|
11.0
|
1.0
|
|
OD2
|
A:ASP202
|
2.3
|
8.7
|
1.0
|
|
O
|
A:LEU184
|
2.3
|
11.0
|
1.0
|
|
OD1
|
A:ASP179
|
2.4
|
9.0
|
1.0
|
|
C
|
A:GLY180
|
3.4
|
9.4
|
1.0
|
|
CD
|
A:GLU205
|
3.4
|
10.3
|
1.0
|
|
CG
|
A:ASP202
|
3.4
|
10.5
|
1.0
|
|
C
|
A:LEU184
|
3.5
|
10.8
|
1.0
|
|
C
|
A:SER182
|
3.5
|
11.7
|
1.0
|
|
CG
|
A:ASP179
|
3.5
|
8.8
|
1.0
|
|
N
|
A:LEU184
|
3.9
|
10.8
|
1.0
|
|
N
|
A:SER182
|
3.9
|
11.0
|
1.0
|
|
CB
|
A:ASP202
|
4.0
|
10.1
|
1.0
|
|
C
|
A:PRO181
|
4.0
|
10.4
|
1.0
|
|
OD2
|
A:ASP179
|
4.1
|
12.3
|
1.0
|
|
N
|
A:GLY180
|
4.1
|
8.6
|
1.0
|
|
CA
|
A:LEU184
|
4.2
|
10.8
|
1.0
|
|
C
|
A:GLY183
|
4.2
|
10.9
|
1.0
|
|
OE1
|
A:GLU205
|
4.2
|
10.2
|
1.0
|
|
CG
|
A:GLU205
|
4.3
|
10.1
|
1.0
|
|
CA
|
A:PRO181
|
4.3
|
9.9
|
1.0
|
|
N
|
A:PRO181
|
4.3
|
9.8
|
1.0
|
|
C
|
A:ASP179
|
4.3
|
8.2
|
1.0
|
|
CA
|
A:SER182
|
4.3
|
11.9
|
1.0
|
|
CA
|
A:GLY180
|
4.3
|
9.2
|
1.0
|
|
OD1
|
A:ASP202
|
4.4
|
8.2
|
1.0
|
|
N
|
A:ASP179
|
4.4
|
8.5
|
1.0
|
|
O
|
A:HOH480
|
4.4
|
19.2
|
1.0
|
|
CB
|
A:LEU184
|
4.5
|
11.1
|
1.0
|
|
N
|
A:GLY183
|
4.5
|
11.0
|
1.0
|
|
O
|
A:PRO181
|
4.5
|
10.5
|
1.0
|
|
N
|
A:LEU185
|
4.6
|
10.3
|
1.0
|
|
CA
|
A:GLY183
|
4.7
|
11.1
|
1.0
|
|
O
|
A:GLY183
|
4.7
|
11.0
|
1.0
|
|
CA
|
A:ASP179
|
4.7
|
8.1
|
1.0
|
|
CB
|
A:ASP179
|
4.7
|
8.7
|
1.0
|
|
O
|
A:ASP179
|
4.7
|
6.4
|
1.0
|
|
CA
|
A:LEU185
|
4.8
|
10.2
|
1.0
|
|
Calcium binding site 3 out
of 8 in 3kry
Go back to
Calcium Binding Sites List in 3kry
Calcium binding site 3 out
of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080
 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 Mmp-13 in Complex with Sc-78080 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2996
b:23.2
occ:1.00
|
O
|
B:ASP162
|
2.3
|
16.4
|
1.0
|
|
O
|
B:GLY196
|
2.3
|
18.7
|
1.0
|
|
O
|
B:HOH295
|
2.4
|
18.3
|
1.0
|
|
O
|
B:ASN194
|
2.5
|
24.2
|
1.0
|
|
OD1
|
B:ASP198
|
2.5
|
14.1
|
1.0
|
|
O
|
B:HOH96
|
2.5
|
17.3
|
1.0
|
|
C
|
B:ASP162
|
3.4
|
16.3
|
1.0
|
|
C
|
B:GLY196
|
3.5
|
18.5
|
1.0
|
|
CG
|
B:ASP198
|
3.5
|
14.1
|
1.0
|
|
C
|
B:ASN194
|
3.7
|
24.1
|
1.0
|
|
C
|
B:TYR195
|
3.9
|
21.9
|
1.0
|
|
O
|
B:TYR195
|
3.9
|
21.1
|
1.0
|
|
OD2
|
B:ASP198
|
3.9
|
14.7
|
1.0
|
|
N
|
B:GLY196
|
4.0
|
20.4
|
1.0
|
|
O
|
B:ALA161
|
4.1
|
17.8
|
1.0
|
|
N
|
B:ASP198
|
4.1
|
15.2
|
1.0
|
|
CA
|
B:ASP162
|
4.3
|
16.9
|
1.0
|
|
CA
|
B:GLY196
|
4.3
|
19.4
|
1.0
|
|
N
|
B:ILE163
|
4.4
|
15.1
|
1.0
|
|
N
|
B:GLY197
|
4.5
|
17.5
|
1.0
|
|
O
|
B:HOH91
|
4.5
|
22.7
|
1.0
|
|
CA
|
B:TYR195
|
4.5
|
23.2
|
1.0
|
|
N
|
B:TYR195
|
4.5
|
23.5
|
1.0
|
|
O
|
B:GLY192
|
4.5
|
22.6
|
1.0
|
|
CA
|
B:GLY197
|
4.6
|
16.8
|
1.0
|
|
C
|
B:GLY197
|
4.6
|
16.0
|
1.0
|
|
CA
|
B:ILE163
|
4.6
|
15.0
|
1.0
|
|
O
|
B:HOH268
|
4.6
|
26.2
|
1.0
|
|
CA
|
B:ASN194
|
4.6
|
24.7
|
1.0
|
|
N
|
B:MET164
|
4.6
|
14.5
|
1.0
|
|
N
|
B:ASN194
|
4.6
|
24.5
|
1.0
|
|
CG
|
B:MET164
|
4.6
|
15.9
|
1.0
|
|
CB
|
B:ASP198
|
4.7
|
14.4
|
1.0
|
|
CA
|
B:ASP198
|
4.8
|
14.5
|
1.0
|
|
CH2
|
B:TRP113
|
4.9
|
19.6
|
1.0
|
|
O
|
B:HOH345
|
4.9
|
30.9
|
1.0
|
|
C
|
B:PRO193
|
5.0
|
24.2
|
1.0
|
|
Calcium binding site 4 out
of 8 in 3kry
Go back to
Calcium Binding Sites List in 3kry
Calcium binding site 4 out
of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080
 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 Mmp-13 in Complex with Sc-78080 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2997
b:14.1
occ:1.00
|
O
|
B:GLY180
|
2.1
|
17.5
|
1.0
|
|
OE2
|
B:GLU205
|
2.3
|
15.6
|
1.0
|
|
OD1
|
B:ASP179
|
2.3
|
17.7
|
1.0
|
|
O
|
B:LEU184
|
2.3
|
16.5
|
1.0
|
|
O
|
B:SER182
|
2.4
|
18.6
|
1.0
|
|
OD2
|
B:ASP202
|
2.4
|
12.6
|
1.0
|
|
C
|
B:GLY180
|
3.4
|
17.5
|
1.0
|
|
CG
|
B:ASP202
|
3.5
|
14.0
|
1.0
|
|
C
|
B:LEU184
|
3.5
|
16.4
|
1.0
|
|
CG
|
B:ASP179
|
3.5
|
15.9
|
1.0
|
|
CD
|
B:GLU205
|
3.5
|
16.4
|
1.0
|
|
C
|
B:SER182
|
3.5
|
19.3
|
1.0
|
|
N
|
B:LEU184
|
3.9
|
17.2
|
1.0
|
|
N
|
B:SER182
|
4.0
|
19.4
|
1.0
|
|
OD2
|
B:ASP179
|
4.0
|
19.0
|
1.0
|
|
C
|
B:PRO181
|
4.0
|
18.9
|
1.0
|
|
N
|
B:GLY180
|
4.0
|
16.7
|
1.0
|
|
CB
|
B:ASP202
|
4.1
|
13.3
|
1.0
|
|
CA
|
B:LEU184
|
4.1
|
17.1
|
1.0
|
|
C
|
B:GLY183
|
4.2
|
17.8
|
1.0
|
|
C
|
B:ASP179
|
4.3
|
16.1
|
1.0
|
|
CA
|
B:GLY180
|
4.3
|
17.2
|
1.0
|
|
N
|
B:PRO181
|
4.3
|
18.1
|
1.0
|
|
N
|
B:ASP179
|
4.3
|
15.7
|
1.0
|
|
CA
|
B:SER182
|
4.3
|
19.8
|
1.0
|
|
OE1
|
B:GLU205
|
4.3
|
17.3
|
1.0
|
|
CA
|
B:PRO181
|
4.4
|
18.5
|
1.0
|
|
O
|
B:PRO181
|
4.4
|
19.7
|
1.0
|
|
OD1
|
B:ASP202
|
4.4
|
11.5
|
1.0
|
|
CG
|
B:GLU205
|
4.4
|
15.2
|
1.0
|
|
CB
|
B:LEU184
|
4.4
|
17.1
|
1.0
|
|
N
|
B:GLY183
|
4.5
|
18.4
|
1.0
|
|
N
|
B:LEU185
|
4.6
|
15.3
|
1.0
|
|
CA
|
B:ASP179
|
4.6
|
15.8
|
1.0
|
|
CA
|
B:GLY183
|
4.6
|
18.2
|
1.0
|
|
CB
|
B:ASP179
|
4.7
|
16.3
|
1.0
|
|
O
|
B:GLY183
|
4.7
|
17.4
|
1.0
|
|
O
|
B:ASP179
|
4.8
|
15.4
|
1.0
|
|
CA
|
B:LEU185
|
4.9
|
15.0
|
1.0
|
|
Calcium binding site 5 out
of 8 in 3kry
Go back to
Calcium Binding Sites List in 3kry
Calcium binding site 5 out
of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080
 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 Mmp-13 in Complex with Sc-78080 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca3996
b:18.9
occ:1.00
|
O
|
C:ASP162
|
2.3
|
14.9
|
1.0
|
|
O
|
C:GLY196
|
2.3
|
17.7
|
1.0
|
|
OD1
|
C:ASP198
|
2.4
|
14.1
|
1.0
|
|
O
|
C:ASN194
|
2.4
|
24.3
|
1.0
|
|
O
|
C:HOH438
|
2.4
|
13.4
|
1.0
|
|
O
|
C:HOH283
|
2.5
|
16.9
|
1.0
|
|
CG
|
C:ASP198
|
3.4
|
15.2
|
1.0
|
|
C
|
C:ASP162
|
3.5
|
15.8
|
1.0
|
|
C
|
C:GLY196
|
3.5
|
18.2
|
1.0
|
|
C
|
C:ASN194
|
3.5
|
24.0
|
1.0
|
|
OD2
|
C:ASP198
|
3.9
|
16.9
|
1.0
|
|
C
|
C:TYR195
|
4.0
|
21.6
|
1.0
|
|
N
|
C:GLY196
|
4.0
|
20.3
|
1.0
|
|
O
|
C:ALA161
|
4.1
|
17.0
|
1.0
|
|
N
|
C:ASP198
|
4.1
|
15.5
|
1.0
|
|
O
|
C:TYR195
|
4.2
|
21.2
|
1.0
|
|
CA
|
C:ASP162
|
4.2
|
16.1
|
1.0
|
|
CA
|
C:GLY196
|
4.3
|
19.2
|
1.0
|
|
O
|
C:GLY192
|
4.3
|
23.3
|
1.0
|
|
N
|
C:TYR195
|
4.3
|
23.3
|
1.0
|
|
O
|
C:HOH291
|
4.3
|
17.0
|
1.0
|
|
CA
|
C:TYR195
|
4.4
|
22.9
|
1.0
|
|
N
|
C:ASN194
|
4.4
|
24.2
|
1.0
|
|
CA
|
C:ASN194
|
4.4
|
24.6
|
1.0
|
|
N
|
C:GLY197
|
4.5
|
17.5
|
1.0
|
|
N
|
C:ILE163
|
4.5
|
15.5
|
1.0
|
|
CB
|
C:ASP198
|
4.6
|
15.1
|
1.0
|
|
CA
|
C:GLY197
|
4.6
|
16.7
|
1.0
|
|
C
|
C:GLY197
|
4.6
|
16.4
|
1.0
|
|
C
|
C:PRO193
|
4.7
|
24.1
|
1.0
|
|
N
|
C:MET164
|
4.7
|
15.0
|
1.0
|
|
CA
|
C:ILE163
|
4.7
|
15.4
|
1.0
|
|
CA
|
C:ASP198
|
4.7
|
15.4
|
1.0
|
|
CG
|
C:MET164
|
4.8
|
15.8
|
1.0
|
|
O
|
C:PRO193
|
4.8
|
24.1
|
1.0
|
|
O
|
C:HOH279
|
4.8
|
25.0
|
1.0
|
|
CH2
|
C:TRP113
|
5.0
|
23.3
|
1.0
|
|
Calcium binding site 6 out
of 8 in 3kry
Go back to
Calcium Binding Sites List in 3kry
Calcium binding site 6 out
of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080
 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 Mmp-13 in Complex with Sc-78080 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca3997
b:17.7
occ:1.00
|
OE2
|
C:GLU205
|
2.2
|
20.5
|
1.0
|
|
O
|
C:LEU184
|
2.2
|
20.1
|
1.0
|
|
OD1
|
C:ASP179
|
2.2
|
18.2
|
1.0
|
|
O
|
C:GLY180
|
2.3
|
20.2
|
1.0
|
|
O
|
C:SER182
|
2.3
|
21.9
|
1.0
|
|
OD2
|
C:ASP202
|
2.3
|
14.3
|
1.0
|
|
C
|
C:LEU184
|
3.4
|
19.2
|
1.0
|
|
CG
|
C:ASP179
|
3.4
|
18.1
|
1.0
|
|
CD
|
C:GLU205
|
3.4
|
17.6
|
1.0
|
|
CG
|
C:ASP202
|
3.4
|
16.2
|
1.0
|
|
C
|
C:SER182
|
3.5
|
21.9
|
1.0
|
|
C
|
C:GLY180
|
3.5
|
20.2
|
1.0
|
|
N
|
C:LEU184
|
3.9
|
20.1
|
1.0
|
|
OD2
|
C:ASP179
|
3.9
|
18.6
|
1.0
|
|
N
|
C:SER182
|
4.0
|
22.0
|
1.0
|
|
N
|
C:GLY180
|
4.0
|
19.0
|
1.0
|
|
CB
|
C:ASP202
|
4.1
|
15.1
|
1.0
|
|
CA
|
C:LEU184
|
4.1
|
19.9
|
1.0
|
|
C
|
C:PRO181
|
4.1
|
21.6
|
1.0
|
|
N
|
C:ASP179
|
4.2
|
18.5
|
1.0
|
|
CA
|
C:SER182
|
4.2
|
22.2
|
1.0
|
|
OE1
|
C:GLU205
|
4.3
|
18.6
|
1.0
|
|
CG
|
C:GLU205
|
4.3
|
18.4
|
1.0
|
|
C
|
C:ASP179
|
4.3
|
18.8
|
1.0
|
|
C
|
C:GLY183
|
4.3
|
20.2
|
1.0
|
|
CA
|
C:GLY180
|
4.4
|
19.7
|
1.0
|
|
CB
|
C:LEU184
|
4.4
|
19.9
|
1.0
|
|
OD1
|
C:ASP202
|
4.4
|
16.1
|
1.0
|
|
O
|
C:PRO181
|
4.4
|
21.9
|
1.0
|
|
N
|
C:LEU185
|
4.4
|
18.6
|
1.0
|
|
N
|
C:GLY183
|
4.5
|
21.2
|
1.0
|
|
N
|
C:PRO181
|
4.5
|
20.8
|
1.0
|
|
CA
|
C:PRO181
|
4.6
|
21.4
|
1.0
|
|
CB
|
C:ASP179
|
4.6
|
18.4
|
1.0
|
|
CA
|
C:ASP179
|
4.6
|
18.6
|
1.0
|
|
CA
|
C:GLY183
|
4.6
|
20.9
|
1.0
|
|
CA
|
C:LEU185
|
4.7
|
17.9
|
1.0
|
|
O
|
C:ASP179
|
4.9
|
18.6
|
1.0
|
|
O
|
C:GLY183
|
4.9
|
19.9
|
1.0
|
|
Calcium binding site 7 out
of 8 in 3kry
Go back to
Calcium Binding Sites List in 3kry
Calcium binding site 7 out
of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080
 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 Mmp-13 in Complex with Sc-78080 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca4996
b:16.9
occ:1.00
|
O
|
D:ASN194
|
2.2
|
20.6
|
1.0
|
|
O
|
D:ASP162
|
2.3
|
14.3
|
1.0
|
|
O
|
D:GLY196
|
2.3
|
16.2
|
1.0
|
|
OD1
|
D:ASP198
|
2.4
|
12.7
|
1.0
|
|
O
|
D:HOH286
|
2.4
|
12.1
|
1.0
|
|
O
|
D:HOH305
|
2.4
|
15.4
|
1.0
|
|
CG
|
D:ASP198
|
3.4
|
14.7
|
1.0
|
|
C
|
D:GLY196
|
3.4
|
16.8
|
1.0
|
|
C
|
D:ASP162
|
3.4
|
15.1
|
1.0
|
|
C
|
D:ASN194
|
3.5
|
21.0
|
1.0
|
|
OD2
|
D:ASP198
|
3.8
|
15.9
|
1.0
|
|
C
|
D:TYR195
|
3.9
|
19.3
|
1.0
|
|
N
|
D:GLY196
|
3.9
|
18.4
|
1.0
|
|
O
|
D:ALA161
|
4.1
|
16.9
|
1.0
|
|
N
|
D:ASP198
|
4.1
|
15.2
|
1.0
|
|
O
|
D:TYR195
|
4.2
|
18.5
|
1.0
|
|
O
|
D:HOH312
|
4.2
|
17.7
|
1.0
|
|
CA
|
D:GLY196
|
4.2
|
17.5
|
1.0
|
|
CA
|
D:ASP162
|
4.2
|
15.8
|
1.0
|
|
O
|
D:GLY192
|
4.3
|
20.6
|
1.0
|
|
N
|
D:ASN194
|
4.3
|
21.0
|
1.0
|
|
N
|
D:TYR195
|
4.4
|
20.4
|
1.0
|
|
CA
|
D:ASN194
|
4.4
|
21.5
|
1.0
|
|
CA
|
D:TYR195
|
4.4
|
20.2
|
1.0
|
|
N
|
D:GLY197
|
4.4
|
16.3
|
1.0
|
|
N
|
D:ILE163
|
4.5
|
14.9
|
1.0
|
|
CB
|
D:ASP198
|
4.6
|
15.0
|
1.0
|
|
CA
|
D:GLY197
|
4.6
|
15.9
|
1.0
|
|
C
|
D:PRO193
|
4.6
|
21.0
|
1.0
|
|
CA
|
D:ILE163
|
4.7
|
14.8
|
1.0
|
|
N
|
D:MET164
|
4.7
|
14.0
|
1.0
|
|
C
|
D:GLY197
|
4.7
|
15.7
|
1.0
|
|
CG
|
D:MET164
|
4.7
|
14.7
|
1.0
|
|
CA
|
D:ASP198
|
4.7
|
15.0
|
1.0
|
|
O
|
D:HOH321
|
4.8
|
13.2
|
0.5
|
|
O
|
D:PRO193
|
4.9
|
20.9
|
1.0
|
|
CH2
|
D:TRP113
|
4.9
|
21.4
|
1.0
|
|
Calcium binding site 8 out
of 8 in 3kry
Go back to
Calcium Binding Sites List in 3kry
Calcium binding site 8 out
of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080
 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 Mmp-13 in Complex with Sc-78080 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca4997
b:17.9
occ:1.00
|
OE2
|
D:GLU205
|
2.2
|
16.3
|
1.0
|
|
O
|
D:LEU184
|
2.3
|
21.1
|
1.0
|
|
OD1
|
D:ASP179
|
2.3
|
20.1
|
1.0
|
|
OD2
|
D:ASP202
|
2.3
|
14.2
|
1.0
|
|
O
|
D:SER182
|
2.3
|
22.8
|
1.0
|
|
O
|
D:GLY180
|
2.3
|
21.1
|
1.0
|
|
CG
|
D:ASP202
|
3.4
|
15.4
|
1.0
|
|
C
|
D:LEU184
|
3.4
|
20.5
|
1.0
|
|
C
|
D:SER182
|
3.5
|
22.8
|
1.0
|
|
CG
|
D:ASP179
|
3.5
|
20.1
|
1.0
|
|
CD
|
D:GLU205
|
3.5
|
16.8
|
1.0
|
|
C
|
D:GLY180
|
3.6
|
21.5
|
1.0
|
|
N
|
D:SER182
|
3.9
|
22.7
|
1.0
|
|
N
|
D:LEU184
|
4.0
|
21.4
|
1.0
|
|
C
|
D:PRO181
|
4.1
|
22.4
|
1.0
|
|
OD2
|
D:ASP179
|
4.1
|
20.8
|
1.0
|
|
CB
|
D:ASP202
|
4.1
|
14.4
|
1.0
|
|
N
|
D:GLY180
|
4.1
|
20.7
|
1.0
|
|
CA
|
D:LEU184
|
4.1
|
20.8
|
1.0
|
|
N
|
D:ASP179
|
4.2
|
19.0
|
1.0
|
|
CA
|
D:SER182
|
4.2
|
22.8
|
1.0
|
|
C
|
D:ASP179
|
4.3
|
20.2
|
1.0
|
|
CG
|
D:GLU205
|
4.3
|
17.6
|
1.0
|
|
C
|
D:GLY183
|
4.3
|
21.5
|
1.0
|
|
OE1
|
D:GLU205
|
4.3
|
17.9
|
1.0
|
|
O
|
D:PRO181
|
4.4
|
23.1
|
1.0
|
|
OD1
|
D:ASP202
|
4.4
|
14.5
|
1.0
|
|
CB
|
D:LEU184
|
4.4
|
21.0
|
1.0
|
|
CA
|
D:GLY180
|
4.5
|
21.1
|
1.0
|
|
N
|
D:GLY183
|
4.5
|
22.2
|
1.0
|
|
N
|
D:PRO181
|
4.5
|
21.8
|
1.0
|
|
N
|
D:LEU185
|
4.5
|
19.7
|
1.0
|
|
CA
|
D:PRO181
|
4.5
|
22.2
|
1.0
|
|
CA
|
D:ASP179
|
4.6
|
19.9
|
1.0
|
|
CB
|
D:ASP179
|
4.6
|
19.8
|
1.0
|
|
CA
|
D:GLY183
|
4.7
|
22.1
|
1.0
|
|
O
|
D:ASP179
|
4.7
|
20.7
|
1.0
|
|
CA
|
D:LEU185
|
4.7
|
19.3
|
1.0
|
|
O
|
D:HOH337
|
4.8
|
20.7
|
1.0
|
|
O
|
D:GLY183
|
4.9
|
22.1
|
1.0
|
|
Reference:
D.P.Becker,
T.E.Barta,
L.J.Bedell,
T.L.Boehm,
B.R.Bond,
J.Carroll,
C.P.Carron,
G.A.Decrescenzo,
A.M.Easton,
J.N.Freskos,
C.L.Funckes-Shippy,
M.Heron,
S.Hockerman,
C.P.Howard,
J.R.Kiefer,
M.H.Li,
K.J.Mathis,
J.J.Mcdonald,
P.P.Mehta,
G.E.Munie,
T.Sunyer,
C.A.Swearingen,
C.I.Villamil,
D.Welsch,
J.M.Williams,
Y.Yu,
J.Yao.
Orally-Active Mmp-1 Sparing Alpha-Tetrahydropyranyl and Alpha-Piperidinyl Sulfone Matrix Metalloproteinase (Mmp) Inhibitors with Efficacy in Cancer, Arthritis, and Cardiovascular Disease J.Med.Chem. V. 53 6653 2010.
ISSN: ISSN 0022-2623
PubMed: 20726512
DOI: 10.1021/JM100669J
Page generated: Sat Dec 12 04:18:03 2020
|
