Calcium in PDB 6sb9: Thermolysin in Complex with J28
Enzymatic activity of Thermolysin in Complex with J28
All present enzymatic activity of Thermolysin in Complex with J28:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with J28, PDB code: 6sb9
was solved by
F.Magari,
A.Heine,
G.Klebe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.42 /
1.30
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.831,
92.831,
129.129,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
12.7 /
15.1
|
Other elements in 6sb9:
The structure of Thermolysin in Complex with J28 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin in Complex with J28
(pdb code 6sb9). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Thermolysin in Complex with J28, PDB code: 6sb9:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6sb9
Go back to
Calcium Binding Sites List in 6sb9
Calcium binding site 1 out
of 4 in the Thermolysin in Complex with J28
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Thermolysin in Complex with J28 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:10.4
occ:1.00
|
O
|
E:GLN61
|
2.3
|
10.2
|
1.0
|
|
O
|
E:HOH736
|
2.4
|
13.1
|
1.0
|
|
OD1
|
E:ASP59
|
2.4
|
11.9
|
1.0
|
|
OD1
|
E:ASP57
|
2.4
|
10.9
|
1.0
|
|
O
|
E:HOH544
|
2.4
|
12.8
|
1.0
|
|
O
|
E:HOH580
|
2.4
|
11.7
|
1.0
|
|
OD2
|
E:ASP57
|
2.6
|
10.1
|
1.0
|
|
CG
|
E:ASP57
|
2.8
|
9.6
|
1.0
|
|
H
|
E:GLN61
|
3.3
|
11.9
|
1.0
|
|
CG
|
E:ASP59
|
3.4
|
12.7
|
1.0
|
|
C
|
E:GLN61
|
3.5
|
9.5
|
1.0
|
|
H
|
E:ASP59
|
3.5
|
13.4
|
1.0
|
|
HB2
|
E:GLN61
|
3.7
|
15.4
|
1.0
|
|
OD2
|
E:ASP59
|
3.8
|
15.2
|
1.0
|
|
O
|
E:HOH655
|
4.0
|
17.7
|
1.0
|
|
N
|
E:GLN61
|
4.0
|
9.9
|
1.0
|
|
HA
|
E:PHE62
|
4.0
|
10.6
|
1.0
|
|
CA
|
E:GLN61
|
4.2
|
10.4
|
1.0
|
|
H
|
E:ALA58
|
4.3
|
13.0
|
1.0
|
|
N
|
E:ASP59
|
4.3
|
11.2
|
1.0
|
|
CB
|
E:ASP57
|
4.3
|
9.5
|
1.0
|
|
H
|
E:ASN60
|
4.4
|
12.4
|
1.0
|
|
CB
|
E:GLN61
|
4.4
|
12.8
|
1.0
|
|
N
|
E:PHE62
|
4.5
|
8.9
|
1.0
|
|
CB
|
E:ASP59
|
4.6
|
12.3
|
1.0
|
|
O
|
E:HOH531
|
4.6
|
10.2
|
1.0
|
|
OD2
|
E:ASP67
|
4.6
|
10.1
|
1.0
|
|
N
|
E:ASN60
|
4.7
|
10.3
|
1.0
|
|
HB2
|
E:ASP57
|
4.7
|
11.4
|
1.0
|
|
N
|
E:ALA58
|
4.7
|
10.8
|
1.0
|
|
O
|
E:HOH811
|
4.7
|
30.5
|
1.0
|
|
CA
|
E:PHE62
|
4.7
|
8.9
|
1.0
|
|
HB3
|
E:ASP57
|
4.8
|
11.4
|
1.0
|
|
CA
|
E:ASP59
|
4.8
|
11.1
|
1.0
|
|
H
|
E:PHE63
|
4.8
|
12.3
|
1.0
|
|
HA
|
E:ASP57
|
4.9
|
11.6
|
1.0
|
|
C
|
E:ASP59
|
4.9
|
10.7
|
1.0
|
|
HB3
|
E:GLN61
|
4.9
|
15.4
|
1.0
|
|
HB3
|
E:ASP59
|
4.9
|
14.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6sb9
Go back to
Calcium Binding Sites List in 6sb9
Calcium binding site 2 out
of 4 in the Thermolysin in Complex with J28
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Thermolysin in Complex with J28 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:10.6
occ:1.00
|
O
|
E:GLU187
|
2.3
|
11.6
|
0.6
|
|
O
|
E:GLU187
|
2.4
|
11.9
|
0.4
|
|
OD2
|
E:ASP138
|
2.4
|
10.4
|
1.0
|
|
O
|
E:HOH562
|
2.4
|
11.9
|
1.0
|
|
OD1
|
E:ASP185
|
2.4
|
12.0
|
1.0
|
|
OE1
|
E:GLU177
|
2.5
|
11.1
|
1.0
|
|
OE2
|
E:GLU190
|
2.5
|
11.5
|
1.0
|
|
OE1
|
E:GLU190
|
2.5
|
11.2
|
1.0
|
|
OE2
|
E:GLU177
|
2.7
|
11.7
|
1.0
|
|
CD
|
E:GLU190
|
2.8
|
11.0
|
1.0
|
|
CD
|
E:GLU177
|
2.9
|
11.1
|
1.0
|
|
CG
|
E:ASP138
|
3.4
|
10.8
|
1.0
|
|
C
|
E:GLU187
|
3.4
|
11.8
|
0.6
|
|
C
|
E:GLU187
|
3.4
|
12.0
|
0.4
|
|
CG
|
E:ASP185
|
3.4
|
12.1
|
1.0
|
|
HB3
|
E:ASP138
|
3.6
|
12.6
|
1.0
|
|
HA
|
E:ILE188
|
3.6
|
13.3
|
1.0
|
|
H
|
E:GLU187
|
3.7
|
16.1
|
0.4
|
|
H
|
E:GLU187
|
3.8
|
16.1
|
0.6
|
|
HB2
|
E:GLU187
|
3.8
|
18.9
|
0.4
|
|
CA
|
E:CA404
|
3.8
|
12.3
|
1.0
|
|
H
|
E:GLY189
|
3.8
|
13.1
|
1.0
|
|
OD2
|
E:ASP185
|
3.8
|
13.1
|
1.0
|
|
CB
|
E:ASP138
|
4.0
|
10.5
|
1.0
|
|
O
|
E:ASP185
|
4.1
|
12.4
|
1.0
|
|
H
|
E:ASP185
|
4.2
|
14.9
|
1.0
|
|
H
|
E:GLU190
|
4.2
|
13.3
|
1.0
|
|
N
|
E:GLU187
|
4.2
|
13.4
|
0.4
|
|
N
|
E:ILE188
|
4.2
|
11.3
|
1.0
|
|
N
|
E:GLU187
|
4.2
|
13.4
|
0.6
|
|
HB2
|
E:ASP138
|
4.2
|
12.6
|
1.0
|
|
HB2
|
E:GLU187
|
4.3
|
19.6
|
0.6
|
|
CA
|
E:GLU187
|
4.3
|
13.7
|
0.4
|
|
HD13
|
E:ILE188
|
4.3
|
17.3
|
1.0
|
|
OD1
|
E:ASP138
|
4.3
|
12.7
|
1.0
|
|
O
|
E:HOH639
|
4.3
|
44.2
|
1.0
|
|
CA
|
E:ILE188
|
4.3
|
11.1
|
1.0
|
|
CA
|
E:GLU187
|
4.3
|
13.7
|
0.6
|
|
CG
|
E:GLU190
|
4.3
|
12.3
|
1.0
|
|
CG
|
E:GLU177
|
4.4
|
11.5
|
1.0
|
|
N
|
E:GLY189
|
4.4
|
10.9
|
1.0
|
|
O
|
E:HOH594
|
4.4
|
15.6
|
1.0
|
|
CB
|
E:GLU187
|
4.5
|
15.7
|
0.4
|
|
C
|
E:ASP185
|
4.6
|
12.3
|
1.0
|
|
HG3
|
E:GLU190
|
4.6
|
14.8
|
1.0
|
|
HB2
|
E:GLU177
|
4.7
|
13.2
|
1.0
|
|
CB
|
E:ASP185
|
4.7
|
12.8
|
1.0
|
|
N
|
E:ASP185
|
4.7
|
12.4
|
1.0
|
|
HB3
|
E:GLU177
|
4.8
|
13.2
|
1.0
|
|
HG2
|
E:GLU190
|
4.8
|
14.8
|
1.0
|
|
C
|
E:ILE188
|
4.8
|
11.4
|
1.0
|
|
CB
|
E:GLU187
|
4.8
|
16.4
|
0.6
|
|
HG2
|
E:GLU177
|
4.8
|
13.8
|
1.0
|
|
CB
|
E:GLU177
|
4.9
|
11.0
|
1.0
|
|
HA
|
E:THR174
|
4.9
|
11.7
|
1.0
|
|
HG3
|
E:GLU177
|
4.9
|
13.8
|
1.0
|
|
O
|
E:HOH545
|
4.9
|
13.4
|
1.0
|
|
HB3
|
E:GLU190
|
4.9
|
14.0
|
1.0
|
|
CA
|
E:ASP185
|
5.0
|
12.3
|
1.0
|
|
N
|
E:GLU190
|
5.0
|
11.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6sb9
Go back to
Calcium Binding Sites List in 6sb9
Calcium binding site 3 out
of 4 in the Thermolysin in Complex with J28
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Thermolysin in Complex with J28 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca404
b:12.3
occ:1.00
|
O
|
E:ASN183
|
2.3
|
14.2
|
1.0
|
|
OD2
|
E:ASP185
|
2.3
|
13.1
|
1.0
|
|
O
|
E:HOH545
|
2.3
|
13.4
|
1.0
|
|
OE2
|
E:GLU190
|
2.3
|
11.5
|
1.0
|
|
O
|
E:HOH556
|
2.3
|
14.4
|
1.0
|
|
OE2
|
E:GLU177
|
2.4
|
11.7
|
1.0
|
|
CG
|
E:ASP185
|
3.2
|
12.1
|
1.0
|
|
CD
|
E:GLU177
|
3.2
|
11.1
|
1.0
|
|
CD
|
E:GLU190
|
3.3
|
11.0
|
1.0
|
|
C
|
E:ASN183
|
3.5
|
14.6
|
1.0
|
|
HA
|
E:PRO184
|
3.5
|
15.6
|
1.0
|
|
HG3
|
E:GLU190
|
3.6
|
14.8
|
1.0
|
|
OD1
|
E:ASP185
|
3.6
|
12.0
|
1.0
|
|
HB2
|
E:ASN183
|
3.7
|
22.5
|
1.0
|
|
OE1
|
E:GLU177
|
3.8
|
11.1
|
1.0
|
|
CA
|
E:CA403
|
3.8
|
10.6
|
1.0
|
|
HG2
|
E:GLU190
|
3.8
|
14.8
|
1.0
|
|
CG
|
E:GLU190
|
3.8
|
12.3
|
1.0
|
|
HB3
|
E:ASN183
|
3.8
|
22.5
|
1.0
|
|
H
|
E:ASP185
|
4.0
|
14.9
|
1.0
|
|
CA
|
E:PRO184
|
4.1
|
13.0
|
1.0
|
|
N
|
E:ASP185
|
4.1
|
12.4
|
1.0
|
|
CB
|
E:ASN183
|
4.1
|
18.8
|
1.0
|
|
O
|
E:HOH663
|
4.2
|
39.6
|
1.0
|
|
OD2
|
E:ASP191
|
4.2
|
15.4
|
1.0
|
|
HG2
|
E:GLU177
|
4.2
|
13.8
|
1.0
|
|
CG
|
E:GLU177
|
4.2
|
11.5
|
1.0
|
|
C
|
E:PRO184
|
4.2
|
12.8
|
1.0
|
|
OD1
|
E:ASP191
|
4.2
|
14.7
|
1.0
|
|
N
|
E:PRO184
|
4.3
|
13.1
|
1.0
|
|
OE1
|
E:GLU190
|
4.3
|
11.2
|
1.0
|
|
HG3
|
E:GLU177
|
4.3
|
13.8
|
1.0
|
|
O
|
E:LYS182
|
4.3
|
16.6
|
1.0
|
|
CB
|
E:ASP185
|
4.4
|
12.8
|
1.0
|
|
HB3
|
E:ASP185
|
4.4
|
15.4
|
1.0
|
|
O
|
E:HOH785
|
4.4
|
35.8
|
1.0
|
|
CA
|
E:ASN183
|
4.4
|
16.3
|
1.0
|
|
O
|
E:HOH639
|
4.5
|
44.2
|
1.0
|
|
CG
|
E:ASP191
|
4.5
|
14.0
|
1.0
|
|
O
|
E:PRO184
|
4.9
|
14.8
|
1.0
|
|
CA
|
E:ASP185
|
4.9
|
12.3
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6sb9
Go back to
Calcium Binding Sites List in 6sb9
Calcium binding site 4 out
of 4 in the Thermolysin in Complex with J28
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Thermolysin in Complex with J28 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca405
b:14.7
occ:1.00
|
O
|
E:ILE197
|
2.3
|
20.0
|
1.0
|
|
O
|
E:TYR193
|
2.4
|
14.0
|
1.0
|
|
OG1
|
E:THR194
|
2.4
|
15.6
|
1.0
|
|
OD1
|
E:ASP200
|
2.4
|
14.6
|
1.0
|
|
O
|
E:HOH695
|
2.4
|
22.9
|
1.0
|
|
O
|
E:HOH566
|
2.4
|
15.0
|
1.0
|
|
O
|
E:THR194
|
2.4
|
16.6
|
1.0
|
|
C
|
E:THR194
|
3.2
|
15.8
|
1.0
|
|
C
|
E:TYR193
|
3.4
|
13.7
|
1.0
|
|
C
|
E:ILE197
|
3.4
|
21.1
|
1.0
|
|
CG
|
E:ASP200
|
3.5
|
15.5
|
1.0
|
|
CB
|
E:THR194
|
3.5
|
16.1
|
1.0
|
|
HB
|
E:ILE197
|
3.5
|
28.0
|
1.0
|
|
H
|
E:ILE197
|
3.6
|
27.9
|
1.0
|
|
CA
|
E:THR194
|
3.7
|
15.6
|
1.0
|
|
HB
|
E:THR194
|
3.7
|
19.4
|
1.0
|
|
OD2
|
E:ASP200
|
3.8
|
16.8
|
1.0
|
|
H
|
E:ASP200
|
3.9
|
19.4
|
1.0
|
|
N
|
E:THR194
|
3.9
|
14.3
|
1.0
|
|
HA
|
E:SER198
|
4.0
|
25.2
|
0.2
|
|
HB3
|
E:TYR193
|
4.0
|
17.4
|
1.0
|
|
HD2
|
E:TYR193
|
4.0
|
20.2
|
1.0
|
|
HA
|
E:SER198
|
4.1
|
27.2
|
0.8
|
|
CA
|
E:ILE197
|
4.2
|
22.3
|
1.0
|
|
N
|
E:ILE197
|
4.2
|
23.3
|
1.0
|
|
CB
|
E:ILE197
|
4.2
|
23.4
|
1.0
|
|
N
|
E:PRO195
|
4.3
|
17.8
|
1.0
|
|
HA
|
E:PRO195
|
4.4
|
23.9
|
1.0
|
|
HG22
|
E:ILE197
|
4.4
|
27.8
|
1.0
|
|
O
|
E:ASP200
|
4.4
|
15.9
|
1.0
|
|
O
|
E:HOH657
|
4.5
|
36.4
|
1.0
|
|
N
|
E:SER198
|
4.5
|
20.9
|
0.2
|
|
N
|
E:SER198
|
4.5
|
21.4
|
0.8
|
|
CA
|
E:TYR193
|
4.6
|
13.3
|
1.0
|
|
H
|
E:GLY199
|
4.6
|
23.1
|
0.2
|
|
HA
|
E:THR194
|
4.6
|
18.8
|
1.0
|
|
CA
|
E:SER198
|
4.6
|
21.0
|
0.2
|
|
O
|
E:GLU190
|
4.6
|
12.6
|
1.0
|
|
CA
|
E:SER198
|
4.6
|
22.7
|
0.8
|
|
N
|
E:ASP200
|
4.7
|
16.1
|
1.0
|
|
CD2
|
E:TYR193
|
4.7
|
16.8
|
1.0
|
|
CB
|
E:TYR193
|
4.7
|
14.5
|
1.0
|
|
CA
|
E:PRO195
|
4.7
|
19.9
|
1.0
|
|
H
|
E:GLY199
|
4.7
|
23.1
|
0.8
|
|
H
|
E:THR194
|
4.8
|
17.2
|
1.0
|
|
CG2
|
E:THR194
|
4.8
|
17.0
|
1.0
|
|
CB
|
E:ASP200
|
4.8
|
15.6
|
1.0
|
|
C
|
E:ASP200
|
4.8
|
14.7
|
1.0
|
|
CG2
|
E:ILE197
|
4.9
|
23.2
|
1.0
|
|
HG23
|
E:THR194
|
4.9
|
20.4
|
1.0
|
|
C
|
E:SER198
|
4.9
|
21.1
|
0.8
|
|
H
|
E:TYR193
|
4.9
|
15.1
|
1.0
|
|
C
|
E:PRO195
|
4.9
|
22.6
|
1.0
|
|
N
|
E:GLY199
|
5.0
|
19.2
|
1.0
|
|
CA
|
E:ASP200
|
5.0
|
15.2
|
1.0
|
|
HG21
|
E:THR194
|
5.0
|
20.4
|
1.0
|
|
Reference:
F.Magari,
A.Heine,
G.Klebe.
Thermolysin in Complex with J28 To Be Published.
Page generated: Tue Jul 16 14:43:38 2024
|
