Calcium in PDB 3elm: Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
Protein crystallography data
The structure of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F, PDB code: 3elm
was solved by
R.Kulathila,
L.Monovich,
J.Koehn,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.56 /
1.90
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
134.500,
36.070,
95.180,
90.00,
130.53,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 3elm:
The structure of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
(pdb code 3elm). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Crystal Structure of Mmp-13 Complexed with Inhibitor 24F, PDB code: 3elm:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 3elm
Go back to
Calcium Binding Sites List in 3elm
Calcium binding site 1 out
of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
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 Complexed with Inhibitor 24F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:13.4
occ:1.00
|
OE2
|
A:GLU205
|
2.2
|
17.6
|
1.0
|
O
|
A:GLY180
|
2.3
|
12.8
|
1.0
|
OD2
|
A:ASP202
|
2.3
|
12.6
|
1.0
|
O
|
A:LEU184
|
2.3
|
14.7
|
1.0
|
O
|
A:SER182
|
2.3
|
18.3
|
1.0
|
OD1
|
A:ASP179
|
2.4
|
15.4
|
1.0
|
CG
|
A:ASP202
|
3.4
|
12.6
|
1.0
|
CD
|
A:GLU205
|
3.4
|
16.6
|
1.0
|
C
|
A:SER182
|
3.4
|
19.9
|
1.0
|
C
|
A:GLY180
|
3.5
|
12.2
|
1.0
|
C
|
A:LEU184
|
3.5
|
15.4
|
1.0
|
CG
|
A:ASP179
|
3.6
|
17.0
|
1.0
|
N
|
A:SER182
|
3.8
|
16.1
|
1.0
|
N
|
A:LEU184
|
3.9
|
14.3
|
1.0
|
C
|
A:PRO181
|
4.0
|
17.1
|
1.0
|
CB
|
A:ASP202
|
4.1
|
12.6
|
1.0
|
N
|
A:GLY180
|
4.1
|
14.2
|
1.0
|
OD2
|
A:ASP179
|
4.1
|
17.2
|
1.0
|
C
|
A:GLY183
|
4.2
|
17.1
|
1.0
|
CA
|
A:SER182
|
4.2
|
20.2
|
1.0
|
CA
|
A:LEU184
|
4.2
|
16.6
|
1.0
|
OE1
|
A:GLU205
|
4.2
|
16.6
|
1.0
|
N
|
A:ASP179
|
4.3
|
14.6
|
1.0
|
C
|
A:ASP179
|
4.3
|
15.1
|
1.0
|
OD1
|
A:ASP202
|
4.3
|
10.2
|
1.0
|
CG
|
A:GLU205
|
4.3
|
13.3
|
1.0
|
O
|
A:PRO181
|
4.3
|
16.9
|
1.0
|
N
|
A:PRO181
|
4.4
|
14.5
|
1.0
|
N
|
A:GLY183
|
4.4
|
19.1
|
1.0
|
CA
|
A:PRO181
|
4.4
|
15.0
|
1.0
|
CA
|
A:GLY180
|
4.4
|
13.5
|
1.0
|
CB
|
A:LEU184
|
4.5
|
18.8
|
1.0
|
O
|
A:HOH1078
|
4.5
|
27.1
|
1.0
|
CA
|
A:GLY183
|
4.6
|
17.4
|
1.0
|
N
|
A:LEU185
|
4.6
|
13.3
|
1.0
|
CA
|
A:ASP179
|
4.6
|
16.1
|
1.0
|
O
|
A:GLY183
|
4.7
|
17.7
|
1.0
|
O
|
A:ASP179
|
4.7
|
15.9
|
1.0
|
CB
|
A:ASP179
|
4.7
|
16.4
|
1.0
|
CA
|
A:LEU185
|
4.8
|
12.3
|
1.0
|
|
Calcium binding site 2 out
of 7 in 3elm
Go back to
Calcium Binding Sites List in 3elm
Calcium binding site 2 out
of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
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 Complexed with Inhibitor 24F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:25.8
occ:1.00
|
O
|
A:HOH1184
|
2.3
|
22.4
|
1.0
|
O
|
A:GLU205
|
2.3
|
14.1
|
1.0
|
OD2
|
A:ASP128
|
2.4
|
12.8
|
1.0
|
OD2
|
A:ASP203
|
2.4
|
15.3
|
1.0
|
O
|
A:ASP203
|
2.5
|
13.5
|
1.0
|
CG
|
A:ASP128
|
3.2
|
16.0
|
1.0
|
C
|
A:ASP203
|
3.3
|
12.8
|
1.0
|
OD1
|
A:ASP128
|
3.3
|
18.1
|
1.0
|
CG
|
A:ASP203
|
3.5
|
17.1
|
1.0
|
C
|
A:GLU205
|
3.6
|
14.6
|
1.0
|
CA
|
A:ASP203
|
3.7
|
12.7
|
1.0
|
OG1
|
A:THR126
|
3.7
|
10.4
|
1.0
|
CD1
|
A:TRP207
|
3.9
|
11.8
|
1.0
|
CB
|
A:ASP203
|
4.0
|
14.5
|
1.0
|
N
|
A:GLU205
|
4.2
|
12.9
|
1.0
|
CA
|
A:THR206
|
4.3
|
13.4
|
1.0
|
N
|
A:ASP204
|
4.3
|
12.6
|
1.0
|
N
|
A:THR206
|
4.4
|
14.0
|
1.0
|
CD
|
A:PRO127
|
4.4
|
12.7
|
1.0
|
C
|
A:ASP204
|
4.4
|
14.1
|
1.0
|
NE1
|
A:TRP207
|
4.5
|
11.4
|
1.0
|
OD1
|
A:ASP203
|
4.5
|
15.8
|
1.0
|
N
|
A:TRP207
|
4.5
|
12.2
|
1.0
|
CA
|
A:GLU205
|
4.6
|
12.8
|
1.0
|
CB
|
A:ASP128
|
4.6
|
12.6
|
1.0
|
CA
|
A:ASP204
|
4.7
|
13.1
|
1.0
|
O
|
A:ASP202
|
4.9
|
13.4
|
1.0
|
C
|
A:THR206
|
5.0
|
13.5
|
1.0
|
CG
|
A:TRP207
|
5.0
|
11.2
|
1.0
|
CB
|
A:THR126
|
5.0
|
10.8
|
1.0
|
|
Calcium binding site 3 out
of 7 in 3elm
Go back to
Calcium Binding Sites List in 3elm
Calcium binding site 3 out
of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
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 Complexed with Inhibitor 24F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:20.5
occ:1.00
|
O
|
A:GLY196
|
2.2
|
13.9
|
1.0
|
O
|
A:ASN194
|
2.4
|
22.7
|
1.0
|
O
|
A:ASP162
|
2.4
|
13.3
|
1.0
|
OD1
|
A:ASP198
|
2.4
|
13.9
|
1.0
|
O
|
A:HOH1183
|
2.5
|
13.2
|
1.0
|
O
|
A:HOH1132
|
2.5
|
14.8
|
1.0
|
C
|
A:GLY196
|
3.4
|
14.7
|
1.0
|
CG
|
A:ASP198
|
3.4
|
15.8
|
1.0
|
C
|
A:ASP162
|
3.5
|
13.0
|
1.0
|
C
|
A:ASN194
|
3.6
|
22.0
|
1.0
|
N
|
A:GLY196
|
3.8
|
16.6
|
1.0
|
C
|
A:TYR195
|
3.8
|
17.9
|
1.0
|
OD2
|
A:ASP198
|
3.9
|
16.6
|
1.0
|
O
|
A:HOH1044
|
4.0
|
25.1
|
1.0
|
N
|
A:ASP198
|
4.1
|
11.2
|
1.0
|
O
|
A:TYR195
|
4.1
|
15.9
|
1.0
|
O
|
A:ALA161
|
4.2
|
15.5
|
1.0
|
CA
|
A:GLY196
|
4.2
|
14.7
|
1.0
|
CA
|
A:TYR195
|
4.2
|
20.6
|
1.0
|
CA
|
A:ASP162
|
4.3
|
13.7
|
1.0
|
N
|
A:TYR195
|
4.4
|
21.5
|
1.0
|
N
|
A:GLY197
|
4.4
|
12.6
|
1.0
|
O
|
A:GLY192
|
4.4
|
17.2
|
1.0
|
N
|
A:ILE163
|
4.5
|
11.8
|
1.0
|
CA
|
A:GLY197
|
4.5
|
12.9
|
1.0
|
C
|
A:GLY197
|
4.5
|
12.4
|
1.0
|
CA
|
A:ASN194
|
4.6
|
22.8
|
1.0
|
CB
|
A:ASP198
|
4.6
|
12.2
|
1.0
|
CH2
|
A:TRP113
|
4.6
|
14.8
|
1.0
|
N
|
A:MET164
|
4.7
|
10.6
|
1.0
|
CA
|
A:ILE163
|
4.7
|
11.8
|
1.0
|
O
|
A:HOH1027
|
4.7
|
20.6
|
1.0
|
CA
|
A:ASP198
|
4.7
|
11.7
|
1.0
|
N
|
A:ASN194
|
4.7
|
20.7
|
1.0
|
CG
|
A:MET164
|
4.8
|
13.6
|
1.0
|
|
Calcium binding site 4 out
of 7 in 3elm
Go back to
Calcium Binding Sites List in 3elm
Calcium binding site 4 out
of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
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 Complexed with Inhibitor 24F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca305
b:32.8
occ:1.00
|
O
|
A:HOH1187
|
2.3
|
23.4
|
1.0
|
O
|
A:THR149
|
2.3
|
13.1
|
1.0
|
O
|
A:SER146
|
2.4
|
14.4
|
1.0
|
O
|
A:HOH1020
|
2.5
|
15.4
|
1.0
|
O
|
A:HOH1003
|
2.5
|
15.6
|
1.0
|
O
|
A:HOH1007
|
2.6
|
15.9
|
1.0
|
C
|
A:THR149
|
3.5
|
12.9
|
1.0
|
C
|
A:SER146
|
3.7
|
15.9
|
1.0
|
N
|
A:THR149
|
4.0
|
14.3
|
1.0
|
O
|
A:HOH1140
|
4.1
|
30.6
|
1.0
|
C
|
A:ASP147
|
4.3
|
16.5
|
1.0
|
CA
|
A:PRO150
|
4.3
|
13.6
|
1.0
|
N
|
A:PRO150
|
4.3
|
13.0
|
1.0
|
CA
|
A:THR149
|
4.4
|
13.1
|
1.0
|
CA
|
A:ASP147
|
4.4
|
16.8
|
1.0
|
O
|
A:HOH1156
|
4.4
|
35.9
|
1.0
|
N
|
A:ASP270
|
4.5
|
16.1
|
1.0
|
O
|
A:ASP147
|
4.5
|
16.1
|
1.0
|
N
|
A:ASP147
|
4.5
|
16.8
|
1.0
|
N
|
A:VAL148
|
4.5
|
14.8
|
1.0
|
CA
|
A:GLY269
|
4.6
|
15.3
|
1.0
|
CA
|
A:SER146
|
4.6
|
15.4
|
1.0
|
O
|
A:LEU151
|
4.7
|
16.3
|
1.0
|
O
|
A:PRO268
|
4.7
|
16.6
|
1.0
|
C
|
A:PRO150
|
4.7
|
15.1
|
1.0
|
N
|
A:LEU151
|
4.9
|
13.9
|
1.0
|
O
|
A:HOH1097
|
4.9
|
21.5
|
1.0
|
C
|
A:VAL148
|
4.9
|
13.2
|
1.0
|
O
|
A:ASP270
|
5.0
|
16.8
|
1.0
|
|
Calcium binding site 5 out
of 7 in 3elm
Go back to
Calcium Binding Sites List in 3elm
Calcium binding site 5 out
of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
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 Complexed with Inhibitor 24F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:17.1
occ:1.00
|
OE2
|
B:GLU205
|
2.2
|
20.8
|
1.0
|
O
|
B:GLY180
|
2.3
|
20.3
|
1.0
|
O
|
B:LEU184
|
2.3
|
16.3
|
1.0
|
OD1
|
B:ASP179
|
2.3
|
18.0
|
1.0
|
OD2
|
B:ASP202
|
2.3
|
14.0
|
1.0
|
O
|
B:SER182
|
2.4
|
21.7
|
1.0
|
C
|
B:LEU184
|
3.4
|
15.8
|
1.0
|
CG
|
B:ASP202
|
3.4
|
15.7
|
1.0
|
C
|
B:SER182
|
3.5
|
23.0
|
1.0
|
CD
|
B:GLU205
|
3.5
|
18.3
|
1.0
|
C
|
B:GLY180
|
3.5
|
19.3
|
1.0
|
CG
|
B:ASP179
|
3.5
|
18.8
|
1.0
|
N
|
B:SER182
|
3.8
|
20.8
|
1.0
|
N
|
B:LEU184
|
3.9
|
18.5
|
1.0
|
C
|
B:PRO181
|
4.0
|
20.0
|
1.0
|
N
|
B:GLY180
|
4.0
|
18.7
|
1.0
|
OD2
|
B:ASP179
|
4.1
|
20.0
|
1.0
|
CB
|
B:ASP202
|
4.1
|
13.5
|
1.0
|
CA
|
B:LEU184
|
4.1
|
17.9
|
1.0
|
CA
|
B:SER182
|
4.2
|
23.3
|
1.0
|
C
|
B:ASP179
|
4.2
|
18.9
|
1.0
|
N
|
B:ASP179
|
4.2
|
16.5
|
1.0
|
C
|
B:GLY183
|
4.2
|
19.0
|
1.0
|
CG
|
B:GLU205
|
4.3
|
19.3
|
1.0
|
OE1
|
B:GLU205
|
4.4
|
19.2
|
1.0
|
O
|
B:PRO181
|
4.4
|
20.5
|
1.0
|
OD1
|
B:ASP202
|
4.4
|
15.5
|
1.0
|
N
|
B:PRO181
|
4.4
|
19.2
|
1.0
|
CA
|
B:GLY180
|
4.4
|
18.4
|
1.0
|
CA
|
B:PRO181
|
4.5
|
19.6
|
1.0
|
CB
|
B:LEU184
|
4.5
|
17.1
|
1.0
|
N
|
B:LEU185
|
4.5
|
13.6
|
1.0
|
N
|
B:GLY183
|
4.5
|
20.7
|
1.0
|
CA
|
B:ASP179
|
4.6
|
18.1
|
1.0
|
CB
|
B:ASP179
|
4.6
|
18.5
|
1.0
|
O
|
B:ASP179
|
4.7
|
17.3
|
1.0
|
CA
|
B:GLY183
|
4.7
|
20.3
|
1.0
|
O
|
B:GLY183
|
4.7
|
17.0
|
1.0
|
CA
|
B:LEU185
|
4.8
|
14.4
|
1.0
|
|
Calcium binding site 6 out
of 7 in 3elm
Go back to
Calcium Binding Sites List in 3elm
Calcium binding site 6 out
of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
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 Complexed with Inhibitor 24F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca303
b:26.7
occ:1.00
|
O
|
B:HOH1143
|
2.2
|
26.9
|
1.0
|
O
|
B:GLU205
|
2.3
|
15.0
|
1.0
|
OD2
|
B:ASP128
|
2.4
|
17.6
|
1.0
|
O
|
B:ASP203
|
2.4
|
16.8
|
1.0
|
OD2
|
B:ASP203
|
2.4
|
13.7
|
1.0
|
O
|
B:HOH1201
|
3.0
|
30.2
|
1.0
|
CG
|
B:ASP128
|
3.1
|
18.2
|
1.0
|
OD1
|
B:ASP128
|
3.2
|
19.1
|
1.0
|
C
|
B:ASP203
|
3.3
|
16.2
|
1.0
|
C
|
B:GLU205
|
3.5
|
16.2
|
1.0
|
CG
|
B:ASP203
|
3.5
|
15.3
|
1.0
|
CA
|
B:ASP203
|
3.7
|
15.3
|
1.0
|
OG1
|
B:THR126
|
3.8
|
11.9
|
1.0
|
CB
|
B:ASP203
|
4.0
|
15.0
|
1.0
|
CD1
|
B:TRP207
|
4.0
|
15.1
|
1.0
|
N
|
B:GLU205
|
4.1
|
14.0
|
1.0
|
CA
|
B:THR206
|
4.1
|
13.9
|
1.0
|
N
|
B:THR206
|
4.3
|
15.2
|
1.0
|
N
|
B:ASP204
|
4.3
|
14.8
|
1.0
|
C
|
B:ASP204
|
4.4
|
15.4
|
1.0
|
NE1
|
B:TRP207
|
4.5
|
13.6
|
1.0
|
CA
|
B:GLU205
|
4.5
|
14.8
|
1.0
|
N
|
B:TRP207
|
4.5
|
14.0
|
1.0
|
OD1
|
B:ASP203
|
4.5
|
15.2
|
1.0
|
CB
|
B:ASP128
|
4.6
|
16.3
|
1.0
|
CA
|
B:ASP204
|
4.6
|
15.0
|
1.0
|
CD
|
B:PRO127
|
4.6
|
12.4
|
1.0
|
O
|
B:HOH1188
|
4.9
|
34.1
|
1.0
|
C
|
B:THR206
|
4.9
|
14.0
|
1.0
|
O
|
B:ASP202
|
4.9
|
14.1
|
1.0
|
|
Calcium binding site 7 out
of 7 in 3elm
Go back to
Calcium Binding Sites List in 3elm
Calcium binding site 7 out
of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F
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 Complexed with Inhibitor 24F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca304
b:18.0
occ:1.00
|
O
|
B:ASP162
|
2.3
|
12.4
|
1.0
|
O
|
B:GLY196
|
2.3
|
14.5
|
1.0
|
O
|
B:HOH1186
|
2.3
|
17.2
|
1.0
|
O
|
B:ASN194
|
2.4
|
20.5
|
1.0
|
OD1
|
B:ASP198
|
2.4
|
12.4
|
1.0
|
O
|
B:HOH1185
|
2.4
|
15.7
|
1.0
|
C
|
B:ASP162
|
3.4
|
13.7
|
1.0
|
C
|
B:GLY196
|
3.4
|
15.3
|
1.0
|
CG
|
B:ASP198
|
3.5
|
13.0
|
1.0
|
C
|
B:ASN194
|
3.5
|
21.7
|
1.0
|
C
|
B:TYR195
|
3.9
|
19.0
|
1.0
|
N
|
B:GLY196
|
3.9
|
16.6
|
1.0
|
OD2
|
B:ASP198
|
4.0
|
13.4
|
1.0
|
O
|
B:TYR195
|
4.1
|
17.8
|
1.0
|
O
|
B:ALA161
|
4.1
|
15.1
|
1.0
|
N
|
B:ASP198
|
4.1
|
13.7
|
1.0
|
O
|
B:HOH1082
|
4.2
|
19.9
|
1.0
|
CA
|
B:ASP162
|
4.2
|
14.7
|
1.0
|
CA
|
B:GLY196
|
4.2
|
14.7
|
1.0
|
CA
|
B:TYR195
|
4.3
|
20.1
|
1.0
|
N
|
B:TYR195
|
4.4
|
18.9
|
1.0
|
O
|
B:GLY192
|
4.4
|
21.4
|
1.0
|
N
|
B:ILE163
|
4.4
|
12.7
|
1.0
|
N
|
B:GLY197
|
4.4
|
13.2
|
1.0
|
CA
|
B:ASN194
|
4.5
|
23.4
|
1.0
|
N
|
B:ASN194
|
4.5
|
23.3
|
1.0
|
CA
|
B:ILE163
|
4.6
|
12.5
|
1.0
|
CA
|
B:GLY197
|
4.6
|
13.6
|
1.0
|
C
|
B:GLY197
|
4.6
|
14.1
|
1.0
|
N
|
B:MET164
|
4.6
|
11.6
|
1.0
|
CB
|
B:ASP198
|
4.6
|
13.1
|
1.0
|
CA
|
B:ASP198
|
4.8
|
14.0
|
1.0
|
O
|
B:HOH1115
|
4.8
|
21.2
|
1.0
|
CH2
|
B:TRP113
|
4.8
|
19.3
|
1.0
|
C
|
B:PRO193
|
4.8
|
23.1
|
1.0
|
CG
|
B:MET164
|
4.8
|
14.2
|
1.0
|
|
Reference:
L.G.Monovich,
R.A.Tommasi,
R.A.Fujimoto,
V.Blancuzzi,
K.Clark,
W.D.Cornell,
R.Doti,
J.Doughty,
J.Fang,
D.Farley,
J.Fitt,
V.Ganu,
R.Goldberg,
R.Goldstein,
S.Lavoie,
R.Kulathila,
W.Macchia,
D.T.Parker,
R.Melton,
E.O'byrne,
G.Pastor,
T.Pellas,
E.Quadros,
N.Reel,
D.M.Roland,
Y.Sakane,
H.Singh,
J.Skiles,
J.Somers,
K.Toscano,
A.Wigg,
S.Zhou,
L.Zhu,
W.C.Shieh,
S.Xue,
L.W.Mcquire.
Discovery of Potent, Selective, and Orally Active Carboxylic Acid Based Inhibitors of Matrix Metalloproteinase-13 J.Med.Chem. V. 52 3523 2009.
ISSN: ISSN 0022-2623
PubMed: 19422229
DOI: 10.1021/JM801394M
Page generated: Sat Jul 13 09:30:45 2024
|