Calcium in PDB 1b3d: Stromelysin-1
Enzymatic activity of Stromelysin-1
All present enzymatic activity of Stromelysin-1:
3.4.24.17;
Protein crystallography data
The structure of Stromelysin-1, PDB code: 1b3d
was solved by
L.Chen,
T.J.Rydel,
C.M.Dunaway,
S.Pikul,
K.M.Dunham,
F.Gu,
B.L.Barnett,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
6.00 /
2.30
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
37.900,
78.800,
105.400,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
25.6 /
26.3
|
Other elements in 1b3d:
The structure of Stromelysin-1 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Stromelysin-1
(pdb code 1b3d). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Stromelysin-1, PDB code: 1b3d:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1b3d
Go back to
Calcium Binding Sites List in 1b3d
Calcium binding site 1 out
of 6 in the Stromelysin-1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Stromelysin-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:3.9
occ:1.00
|
O
|
A:GLY159
|
2.3
|
10.4
|
1.0
|
|
O
|
A:VAL163
|
2.4
|
6.3
|
1.0
|
|
OD2
|
A:ASP181
|
2.4
|
2.0
|
1.0
|
|
O
|
A:GLY161
|
2.5
|
2.3
|
1.0
|
|
OE2
|
A:GLU184
|
2.5
|
6.8
|
1.0
|
|
OD1
|
A:ASP158
|
2.6
|
2.0
|
1.0
|
|
CG
|
A:ASP181
|
3.4
|
2.0
|
1.0
|
|
C
|
A:VAL163
|
3.5
|
3.6
|
1.0
|
|
C
|
A:GLY159
|
3.5
|
8.8
|
1.0
|
|
C
|
A:GLY161
|
3.6
|
2.0
|
1.0
|
|
CD
|
A:GLU184
|
3.7
|
5.6
|
1.0
|
|
CG
|
A:ASP158
|
3.9
|
4.7
|
1.0
|
|
N
|
A:VAL163
|
4.0
|
2.8
|
1.0
|
|
C
|
A:ASP158
|
4.0
|
9.1
|
1.0
|
|
N
|
A:GLY161
|
4.1
|
2.0
|
1.0
|
|
N
|
A:GLY159
|
4.1
|
9.9
|
1.0
|
|
CB
|
A:ASP181
|
4.1
|
2.0
|
1.0
|
|
C
|
A:PRO160
|
4.1
|
3.4
|
1.0
|
|
CA
|
A:VAL163
|
4.2
|
4.1
|
1.0
|
|
N
|
A:ASP158
|
4.2
|
6.2
|
1.0
|
|
O
|
A:ASP158
|
4.3
|
11.6
|
1.0
|
|
OD1
|
A:ASP181
|
4.3
|
2.0
|
1.0
|
|
CA
|
A:GLY161
|
4.4
|
2.0
|
1.0
|
|
CA
|
A:GLY159
|
4.4
|
7.3
|
1.0
|
|
N
|
A:PRO160
|
4.4
|
6.8
|
1.0
|
|
O
|
A:PRO160
|
4.5
|
2.4
|
1.0
|
|
C
|
A:ASN162
|
4.5
|
2.0
|
1.0
|
|
CA
|
A:PRO160
|
4.5
|
3.7
|
1.0
|
|
CA
|
A:ASP158
|
4.5
|
5.1
|
1.0
|
|
N
|
A:LEU164
|
4.5
|
2.6
|
1.0
|
|
CG
|
A:GLU184
|
4.6
|
6.5
|
1.0
|
|
OE1
|
A:GLU184
|
4.6
|
13.7
|
1.0
|
|
CB
|
A:VAL163
|
4.6
|
2.0
|
1.0
|
|
OD2
|
A:ASP158
|
4.6
|
11.7
|
1.0
|
|
N
|
A:ASN162
|
4.7
|
2.0
|
1.0
|
|
CA
|
A:LEU164
|
4.8
|
2.0
|
1.0
|
|
CB
|
A:ASP158
|
4.8
|
4.4
|
1.0
|
|
CA
|
A:ASN162
|
4.9
|
2.0
|
1.0
|
|
O
|
A:HOH311
|
5.0
|
4.0
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1b3d
Go back to
Calcium Binding Sites List in 1b3d
Calcium binding site 2 out
of 6 in the Stromelysin-1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Stromelysin-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:10.7
occ:1.00
|
O
|
A:ASP182
|
2.3
|
7.4
|
1.0
|
|
OD2
|
A:ASP107
|
2.3
|
2.0
|
1.0
|
|
OD1
|
A:ASP107
|
2.5
|
2.0
|
1.0
|
|
O
|
A:GLU184
|
2.5
|
2.0
|
1.0
|
|
O
|
A:HOH322
|
2.6
|
35.3
|
1.0
|
|
OD1
|
A:ASP182
|
2.7
|
7.0
|
1.0
|
|
CG
|
A:ASP107
|
2.8
|
2.0
|
1.0
|
|
C
|
A:ASP182
|
3.3
|
6.2
|
1.0
|
|
CG
|
A:ASP182
|
3.7
|
8.1
|
1.0
|
|
C
|
A:GLU184
|
3.7
|
2.0
|
1.0
|
|
CA
|
A:ASP182
|
3.9
|
5.1
|
1.0
|
|
CB
|
A:ASP182
|
4.1
|
7.5
|
1.0
|
|
OG1
|
A:THR105
|
4.2
|
9.0
|
1.0
|
|
CB
|
A:ASP107
|
4.2
|
4.1
|
1.0
|
|
N
|
A:GLU184
|
4.2
|
7.8
|
1.0
|
|
CA
|
A:GLN185
|
4.3
|
2.7
|
1.0
|
|
N
|
A:ASP183
|
4.4
|
7.1
|
1.0
|
|
N
|
A:GLN185
|
4.4
|
5.6
|
1.0
|
|
CD1
|
A:TRP186
|
4.5
|
2.7
|
1.0
|
|
O
|
A:HOH349
|
4.6
|
18.8
|
1.0
|
|
C
|
A:ASP183
|
4.7
|
8.8
|
1.0
|
|
OE1
|
A:GLN185
|
4.7
|
5.7
|
1.0
|
|
OD2
|
A:ASP182
|
4.7
|
12.8
|
1.0
|
|
CA
|
A:GLU184
|
4.7
|
5.1
|
1.0
|
|
CA
|
A:ASP183
|
4.7
|
8.3
|
1.0
|
|
N
|
A:TRP186
|
4.8
|
6.3
|
1.0
|
|
O
|
A:HOH312
|
4.8
|
26.4
|
1.0
|
|
CG
|
A:PRO106
|
4.9
|
10.9
|
1.0
|
|
NE1
|
A:TRP186
|
5.0
|
2.2
|
1.0
|
|
N
|
A:ASP107
|
5.0
|
8.8
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1b3d
Go back to
Calcium Binding Sites List in 1b3d
Calcium binding site 3 out
of 6 in the Stromelysin-1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Stromelysin-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca305
b:7.3
occ:1.00
|
O
|
A:ASP141
|
2.4
|
2.8
|
1.0
|
|
O
|
A:GLY173
|
2.4
|
3.9
|
1.0
|
|
OD1
|
A:ASP177
|
2.5
|
5.2
|
1.0
|
|
O
|
A:ASN175
|
2.5
|
13.3
|
1.0
|
|
O
|
A:HOH329
|
2.6
|
9.7
|
1.0
|
|
O
|
A:HOH320
|
2.8
|
14.2
|
1.0
|
|
CG
|
A:ASP177
|
3.4
|
2.0
|
1.0
|
|
C
|
A:ASP141
|
3.5
|
3.9
|
1.0
|
|
C
|
A:GLY173
|
3.6
|
5.1
|
1.0
|
|
C
|
A:ASN175
|
3.6
|
10.5
|
1.0
|
|
O
|
A:ALA140
|
3.7
|
5.9
|
1.0
|
|
OD2
|
A:ASP177
|
3.8
|
2.0
|
1.0
|
|
CA
|
A:ASP141
|
4.2
|
5.0
|
1.0
|
|
N
|
A:ASN175
|
4.2
|
9.7
|
1.0
|
|
N
|
A:ASP177
|
4.2
|
4.6
|
1.0
|
|
C
|
A:ILE174
|
4.2
|
9.4
|
1.0
|
|
N
|
A:GLY173
|
4.3
|
6.6
|
1.0
|
|
O
|
A:GLY171
|
4.4
|
7.0
|
1.0
|
|
CA
|
A:GLY173
|
4.4
|
6.0
|
1.0
|
|
O
|
A:ILE174
|
4.5
|
11.4
|
1.0
|
|
CA
|
A:ASN175
|
4.5
|
12.4
|
1.0
|
|
N
|
A:ILE142
|
4.5
|
3.7
|
1.0
|
|
N
|
A:ILE174
|
4.5
|
6.5
|
1.0
|
|
N
|
A:GLY176
|
4.5
|
8.8
|
1.0
|
|
C
|
A:GLY176
|
4.5
|
5.0
|
1.0
|
|
CA
|
A:GLY176
|
4.5
|
7.0
|
1.0
|
|
C
|
A:PRO172
|
4.6
|
6.4
|
1.0
|
|
CA
|
A:ILE174
|
4.6
|
7.0
|
1.0
|
|
CB
|
A:ASP177
|
4.6
|
3.2
|
1.0
|
|
CG
|
A:MET143
|
4.7
|
5.0
|
1.0
|
|
N
|
A:MET143
|
4.7
|
4.0
|
1.0
|
|
C
|
A:ALA140
|
4.8
|
5.0
|
1.0
|
|
O
|
A:PRO172
|
4.8
|
8.0
|
1.0
|
|
CA
|
A:ILE142
|
4.8
|
4.0
|
1.0
|
|
CA
|
A:ASP177
|
4.8
|
6.3
|
1.0
|
|
CH2
|
A:TRP92
|
4.9
|
11.1
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1b3d
Go back to
Calcium Binding Sites List in 1b3d
Calcium binding site 4 out
of 6 in the Stromelysin-1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Stromelysin-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca303
b:6.2
occ:1.00
|
OE2
|
B:GLU184
|
2.2
|
8.2
|
1.0
|
|
O
|
B:GLY159
|
2.3
|
20.6
|
1.0
|
|
OD2
|
B:ASP181
|
2.3
|
8.3
|
1.0
|
|
O
|
B:VAL163
|
2.4
|
11.3
|
1.0
|
|
OD1
|
B:ASP158
|
2.4
|
14.5
|
1.0
|
|
O
|
B:GLY161
|
2.5
|
11.0
|
1.0
|
|
CG
|
B:ASP181
|
3.3
|
9.0
|
1.0
|
|
CD
|
B:GLU184
|
3.4
|
8.8
|
1.0
|
|
C
|
B:VAL163
|
3.4
|
7.0
|
1.0
|
|
C
|
B:GLY159
|
3.5
|
13.9
|
1.0
|
|
CG
|
B:ASP158
|
3.6
|
12.0
|
1.0
|
|
C
|
B:GLY161
|
3.7
|
10.4
|
1.0
|
|
N
|
B:GLY159
|
3.9
|
14.7
|
1.0
|
|
N
|
B:VAL163
|
4.0
|
14.6
|
1.0
|
|
CB
|
B:ASP181
|
4.0
|
7.1
|
1.0
|
|
N
|
B:GLY161
|
4.0
|
12.7
|
1.0
|
|
OE1
|
B:GLU184
|
4.1
|
11.5
|
1.0
|
|
CA
|
B:VAL163
|
4.2
|
8.2
|
1.0
|
|
OD1
|
B:ASP181
|
4.2
|
8.6
|
1.0
|
|
OD2
|
B:ASP158
|
4.3
|
12.7
|
1.0
|
|
C
|
B:ASP158
|
4.3
|
14.2
|
1.0
|
|
C
|
B:PRO160
|
4.3
|
11.9
|
1.0
|
|
CA
|
B:GLY159
|
4.3
|
15.5
|
1.0
|
|
N
|
B:LEU164
|
4.4
|
7.8
|
1.0
|
|
C
|
B:ASN162
|
4.4
|
15.2
|
1.0
|
|
N
|
B:ASP158
|
4.4
|
14.9
|
1.0
|
|
CA
|
B:GLY161
|
4.4
|
11.4
|
1.0
|
|
N
|
B:PRO160
|
4.5
|
12.8
|
1.0
|
|
CG
|
B:GLU184
|
4.5
|
2.0
|
1.0
|
|
CA
|
B:PRO160
|
4.6
|
11.5
|
1.0
|
|
CA
|
B:LEU164
|
4.6
|
5.8
|
1.0
|
|
CA
|
B:ASP158
|
4.6
|
14.7
|
1.0
|
|
CB
|
B:VAL163
|
4.7
|
4.0
|
1.0
|
|
N
|
B:ASN162
|
4.7
|
13.1
|
1.0
|
|
CB
|
B:ASP158
|
4.7
|
15.2
|
1.0
|
|
O
|
B:ASN162
|
4.8
|
17.8
|
1.0
|
|
O
|
B:PRO160
|
4.9
|
12.4
|
1.0
|
|
O
|
B:ASP158
|
4.9
|
15.5
|
1.0
|
|
CA
|
B:ASN162
|
4.9
|
14.3
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1b3d
Go back to
Calcium Binding Sites List in 1b3d
Calcium binding site 5 out
of 6 in the Stromelysin-1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Stromelysin-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca304
b:14.5
occ:1.00
|
OD1
|
B:ASP182
|
2.3
|
3.5
|
1.0
|
|
O
|
B:ASP182
|
2.4
|
7.2
|
1.0
|
|
O
|
B:HOH416
|
2.6
|
13.0
|
1.0
|
|
OD2
|
B:ASP107
|
2.6
|
15.4
|
1.0
|
|
OD1
|
B:ASP107
|
2.6
|
13.7
|
1.0
|
|
O
|
B:GLU184
|
2.7
|
4.7
|
1.0
|
|
O
|
B:HOH424
|
2.7
|
6.1
|
1.0
|
|
CG
|
B:ASP107
|
2.9
|
11.0
|
1.0
|
|
CG
|
B:ASP182
|
3.4
|
2.0
|
1.0
|
|
C
|
B:ASP182
|
3.4
|
7.8
|
1.0
|
|
C
|
B:GLU184
|
3.9
|
5.8
|
1.0
|
|
CA
|
B:ASP182
|
3.9
|
5.5
|
1.0
|
|
OG1
|
B:THR105
|
4.1
|
5.0
|
1.0
|
|
CB
|
B:ASP182
|
4.1
|
2.0
|
1.0
|
|
OD2
|
B:ASP182
|
4.3
|
3.3
|
1.0
|
|
CD1
|
B:TRP186
|
4.3
|
12.9
|
1.0
|
|
N
|
B:GLU184
|
4.4
|
7.0
|
1.0
|
|
CB
|
B:ASP107
|
4.4
|
9.1
|
1.0
|
|
N
|
B:ASP183
|
4.5
|
8.7
|
1.0
|
|
CA
|
B:GLN185
|
4.6
|
11.7
|
1.0
|
|
CD
|
B:PRO106
|
4.7
|
8.4
|
1.0
|
|
O
|
B:HOH415
|
4.7
|
15.0
|
1.0
|
|
N
|
B:GLN185
|
4.7
|
9.1
|
1.0
|
|
NE1
|
B:TRP186
|
4.8
|
10.4
|
1.0
|
|
CA
|
B:ASP183
|
4.8
|
10.1
|
1.0
|
|
N
|
B:TRP186
|
4.8
|
10.8
|
1.0
|
|
C
|
B:ASP183
|
4.8
|
9.7
|
1.0
|
|
CA
|
B:GLU184
|
4.9
|
7.9
|
1.0
|
|
N
|
B:ASP107
|
4.9
|
8.7
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1b3d
Go back to
Calcium Binding Sites List in 1b3d
Calcium binding site 6 out
of 6 in the Stromelysin-1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Stromelysin-1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca305
b:12.3
occ:1.00
|
O
|
B:ASP141
|
2.3
|
4.7
|
1.0
|
|
O
|
B:HOH417
|
2.4
|
2.0
|
1.0
|
|
O
|
B:GLY173
|
2.4
|
4.6
|
1.0
|
|
O
|
B:ASN175
|
2.5
|
7.5
|
1.0
|
|
OD1
|
B:ASP177
|
2.5
|
10.0
|
1.0
|
|
O
|
B:HOH408
|
2.6
|
6.4
|
1.0
|
|
C
|
B:ASP141
|
3.4
|
8.4
|
1.0
|
|
CG
|
B:ASP177
|
3.4
|
9.1
|
1.0
|
|
C
|
B:GLY173
|
3.6
|
4.2
|
1.0
|
|
C
|
B:ASN175
|
3.6
|
8.2
|
1.0
|
|
OD2
|
B:ASP177
|
3.7
|
13.7
|
1.0
|
|
O
|
B:ALA140
|
3.9
|
7.5
|
1.0
|
|
CA
|
B:ASP141
|
4.1
|
8.7
|
1.0
|
|
N
|
B:GLY173
|
4.1
|
6.7
|
1.0
|
|
N
|
B:ASN175
|
4.2
|
9.9
|
1.0
|
|
C
|
B:ILE174
|
4.3
|
9.2
|
1.0
|
|
N
|
B:ASP177
|
4.3
|
5.9
|
1.0
|
|
CA
|
B:GLY173
|
4.3
|
3.1
|
1.0
|
|
C
|
B:GLY176
|
4.4
|
7.3
|
1.0
|
|
N
|
B:ILE142
|
4.4
|
6.6
|
1.0
|
|
O
|
B:ILE174
|
4.5
|
8.5
|
1.0
|
|
CA
|
B:ASN175
|
4.5
|
7.0
|
1.0
|
|
N
|
B:GLY176
|
4.5
|
8.0
|
1.0
|
|
N
|
B:ILE174
|
4.5
|
5.5
|
1.0
|
|
CA
|
B:GLY176
|
4.5
|
7.9
|
1.0
|
|
O
|
B:GLY171
|
4.6
|
9.6
|
1.0
|
|
N
|
B:MET143
|
4.7
|
3.4
|
1.0
|
|
CA
|
B:ILE142
|
4.7
|
4.0
|
1.0
|
|
CB
|
B:ASP177
|
4.7
|
8.1
|
1.0
|
|
CA
|
B:ILE174
|
4.7
|
7.6
|
1.0
|
|
C
|
B:PRO172
|
4.7
|
7.7
|
1.0
|
|
CG
|
B:MET143
|
4.8
|
4.2
|
1.0
|
|
O
|
B:HOH407
|
4.8
|
21.5
|
1.0
|
|
CA
|
B:ASP177
|
4.9
|
7.0
|
1.0
|
|
CH2
|
B:TRP92
|
4.9
|
8.6
|
1.0
|
|
C
|
B:ALA140
|
4.9
|
7.8
|
1.0
|
|
O
|
B:GLY176
|
5.0
|
7.3
|
1.0
|
|
Reference:
L.Chen,
T.J.Rydel,
F.Gu,
C.M.Dunaway,
S.Pikul,
K.M.Dunham,
B.L.Barnett.
Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution: Inhibitor-Induced Conformational Changes. J.Mol.Biol. V. 293 545 1999.
ISSN: ISSN 0022-2836
PubMed: 10543949
DOI: 10.1006/JMBI.1999.3147
Page generated: Sat Dec 12 02:49:15 2020
|
