Calcium in PDB 6sbk: Thermolysin in Complex with Fragment J13
Enzymatic activity of Thermolysin in Complex with Fragment J13
All present enzymatic activity of Thermolysin in Complex with Fragment J13:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with Fragment J13, PDB code: 6sbk
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)
|
46.28 /
1.48
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.561,
92.561,
129.273,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
15 /
16.9
|
Other elements in 6sbk:
The structure of Thermolysin in Complex with Fragment J13 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin in Complex with Fragment J13
(pdb code 6sbk). 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 Fragment J13, PDB code: 6sbk:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6sbk
Go back to
Calcium Binding Sites List in 6sbk
Calcium binding site 1 out
of 4 in the Thermolysin in Complex with Fragment J13
 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 Fragment J13 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:13.1
occ:1.00
|
O
|
E:ASN183
|
2.3
|
15.4
|
1.0
|
|
O
|
E:HOH534
|
2.3
|
14.8
|
1.0
|
|
OD2
|
E:ASP185
|
2.3
|
13.6
|
1.0
|
|
O
|
E:HOH564
|
2.3
|
14.8
|
1.0
|
|
OE2
|
E:GLU190
|
2.4
|
12.7
|
1.0
|
|
OE2
|
E:GLU177
|
2.4
|
12.5
|
1.0
|
|
CD
|
E:GLU177
|
3.2
|
11.4
|
1.0
|
|
CG
|
E:ASP185
|
3.2
|
11.4
|
1.0
|
|
CD
|
E:GLU190
|
3.3
|
12.2
|
1.0
|
|
C
|
E:ASN183
|
3.5
|
16.2
|
1.0
|
|
HG3
|
E:GLU190
|
3.6
|
16.4
|
1.0
|
|
HA
|
E:PRO184
|
3.6
|
15.0
|
1.0
|
|
OD1
|
E:ASP185
|
3.6
|
12.8
|
1.0
|
|
HB2
|
E:ASN183
|
3.8
|
19.5
|
1.0
|
|
OE1
|
E:GLU177
|
3.8
|
11.2
|
1.0
|
|
HG2
|
E:GLU190
|
3.8
|
16.4
|
1.0
|
|
CG
|
E:GLU190
|
3.8
|
13.7
|
1.0
|
|
CA
|
E:CA404
|
3.8
|
11.2
|
1.0
|
|
HB3
|
E:ASN183
|
3.8
|
19.5
|
1.0
|
|
H
|
E:ASP185
|
4.1
|
16.8
|
1.0
|
|
OD2
|
E:ASP191
|
4.1
|
18.2
|
1.0
|
|
CA
|
E:PRO184
|
4.1
|
12.5
|
1.0
|
|
CB
|
E:ASN183
|
4.2
|
16.3
|
1.0
|
|
HG2
|
E:GLU177
|
4.2
|
13.2
|
1.0
|
|
N
|
E:ASP185
|
4.2
|
14.0
|
1.0
|
|
CG
|
E:GLU177
|
4.2
|
11.0
|
1.0
|
|
C
|
E:PRO184
|
4.2
|
14.9
|
1.0
|
|
OD1
|
E:ASP191
|
4.3
|
15.2
|
1.0
|
|
N
|
E:PRO184
|
4.3
|
13.4
|
1.0
|
|
HG3
|
E:GLU177
|
4.3
|
13.2
|
1.0
|
|
OE1
|
E:GLU190
|
4.3
|
11.9
|
1.0
|
|
HB3
|
E:ASP185
|
4.4
|
13.4
|
1.0
|
|
O
|
E:LYS182
|
4.4
|
17.8
|
1.0
|
|
CB
|
E:ASP185
|
4.4
|
11.2
|
1.0
|
|
O
|
E:HOH746
|
4.4
|
37.9
|
1.0
|
|
CA
|
E:ASN183
|
4.5
|
15.2
|
1.0
|
|
CG
|
E:ASP191
|
4.5
|
15.8
|
1.0
|
|
O
|
E:PRO184
|
4.9
|
17.2
|
1.0
|
|
CA
|
E:ASP185
|
4.9
|
12.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6sbk
Go back to
Calcium Binding Sites List in 6sbk
Calcium binding site 2 out
of 4 in the Thermolysin in Complex with Fragment J13
 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 Fragment J13 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:14.5
occ:1.00
|
O
|
E:ILE197
|
2.2
|
16.4
|
1.0
|
|
O
|
E:TYR193
|
2.3
|
14.2
|
1.0
|
|
OG1
|
E:THR194
|
2.4
|
16.1
|
1.0
|
|
OD2
|
E:ASP200
|
2.4
|
15.5
|
1.0
|
|
O
|
E:HOH577
|
2.4
|
13.9
|
1.0
|
|
O
|
E:HOH671
|
2.4
|
24.2
|
1.0
|
|
O
|
E:THR194
|
2.4
|
17.3
|
1.0
|
|
C
|
E:THR194
|
3.2
|
16.1
|
1.0
|
|
C
|
E:TYR193
|
3.3
|
13.3
|
1.0
|
|
CB
|
E:THR194
|
3.4
|
17.3
|
1.0
|
|
CG
|
E:ASP200
|
3.4
|
16.9
|
1.0
|
|
C
|
E:ILE197
|
3.4
|
19.1
|
1.0
|
|
HB
|
E:ILE197
|
3.5
|
30.8
|
1.0
|
|
H
|
E:ILE197
|
3.6
|
29.3
|
1.0
|
|
CA
|
E:THR194
|
3.7
|
14.8
|
1.0
|
|
HB
|
E:THR194
|
3.7
|
20.8
|
1.0
|
|
OD1
|
E:ASP200
|
3.8
|
17.5
|
1.0
|
|
H
|
E:ASP200
|
3.9
|
18.1
|
1.0
|
|
N
|
E:THR194
|
3.9
|
14.0
|
1.0
|
|
HA
|
E:SER198
|
4.0
|
24.1
|
0.6
|
|
HA
|
E:SER198
|
4.1
|
23.8
|
0.4
|
|
HD2
|
E:TYR193
|
4.1
|
20.4
|
1.0
|
|
HB3
|
E:TYR193
|
4.1
|
17.2
|
1.0
|
|
CA
|
E:ILE197
|
4.2
|
19.7
|
1.0
|
|
N
|
E:ILE197
|
4.2
|
24.4
|
1.0
|
|
CB
|
E:ILE197
|
4.3
|
25.7
|
1.0
|
|
N
|
E:PRO195
|
4.3
|
16.5
|
1.0
|
|
HA
|
E:PRO195
|
4.3
|
21.2
|
1.0
|
|
O
|
E:HOH649
|
4.4
|
34.2
|
1.0
|
|
O
|
E:ASP200
|
4.4
|
16.5
|
1.0
|
|
N
|
E:SER198
|
4.5
|
18.1
|
0.6
|
|
N
|
E:SER198
|
4.5
|
21.0
|
0.4
|
|
CA
|
E:TYR193
|
4.5
|
13.6
|
1.0
|
|
O
|
E:HOH717
|
4.5
|
30.7
|
1.0
|
|
HG22
|
E:ILE197
|
4.6
|
27.4
|
1.0
|
|
HA
|
E:THR194
|
4.6
|
17.8
|
1.0
|
|
CA
|
E:SER198
|
4.6
|
20.1
|
0.6
|
|
N
|
E:ASP200
|
4.6
|
15.1
|
1.0
|
|
O
|
E:GLU190
|
4.7
|
13.9
|
1.0
|
|
CA
|
E:SER198
|
4.7
|
19.8
|
0.4
|
|
CD2
|
E:TYR193
|
4.7
|
17.0
|
1.0
|
|
CB
|
E:TYR193
|
4.7
|
14.3
|
1.0
|
|
CA
|
E:PRO195
|
4.7
|
17.7
|
1.0
|
|
H
|
E:GLY199
|
4.7
|
21.8
|
0.4
|
|
CG2
|
E:THR194
|
4.7
|
17.2
|
1.0
|
|
H
|
E:THR194
|
4.7
|
16.8
|
1.0
|
|
H
|
E:GLY199
|
4.7
|
21.8
|
0.6
|
|
CB
|
E:ASP200
|
4.8
|
15.9
|
1.0
|
|
C
|
E:ASP200
|
4.8
|
15.0
|
1.0
|
|
HG23
|
E:THR194
|
4.9
|
20.7
|
1.0
|
|
H
|
E:TYR193
|
4.9
|
14.3
|
1.0
|
|
C
|
E:PRO195
|
4.9
|
21.7
|
1.0
|
|
C
|
E:SER198
|
4.9
|
19.1
|
0.6
|
|
HG21
|
E:THR194
|
5.0
|
20.7
|
1.0
|
|
CG2
|
E:ILE197
|
5.0
|
22.8
|
1.0
|
|
CA
|
E:ASP200
|
5.0
|
16.6
|
1.0
|
|
N
|
E:GLY199
|
5.0
|
18.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6sbk
Go back to
Calcium Binding Sites List in 6sbk
Calcium binding site 3 out
of 4 in the Thermolysin in Complex with Fragment J13
 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 Fragment J13 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca404
b:11.2
occ:1.00
|
O
|
E:GLU187
|
2.2
|
12.9
|
0.6
|
|
OD2
|
E:ASP138
|
2.3
|
10.9
|
1.0
|
|
O
|
E:GLU187
|
2.4
|
11.4
|
0.5
|
|
O
|
E:HOH553
|
2.4
|
12.0
|
1.0
|
|
OE1
|
E:GLU177
|
2.4
|
11.2
|
1.0
|
|
OD1
|
E:ASP185
|
2.5
|
12.8
|
1.0
|
|
OE2
|
E:GLU190
|
2.5
|
12.7
|
1.0
|
|
OE1
|
E:GLU190
|
2.6
|
11.9
|
1.0
|
|
OE2
|
E:GLU177
|
2.8
|
12.5
|
1.0
|
|
CD
|
E:GLU190
|
2.8
|
12.2
|
1.0
|
|
CD
|
E:GLU177
|
2.9
|
11.4
|
1.0
|
|
CG
|
E:ASP138
|
3.4
|
11.8
|
1.0
|
|
C
|
E:GLU187
|
3.4
|
11.5
|
0.6
|
|
C
|
E:GLU187
|
3.4
|
14.0
|
0.5
|
|
CG
|
E:ASP185
|
3.5
|
11.4
|
1.0
|
|
HB3
|
E:ASP138
|
3.6
|
10.5
|
1.0
|
|
HA
|
E:ILE188
|
3.6
|
15.0
|
1.0
|
|
H
|
E:GLU187
|
3.7
|
16.2
|
0.6
|
|
H
|
E:GLU187
|
3.7
|
16.7
|
0.5
|
|
H
|
E:GLY189
|
3.8
|
14.0
|
1.0
|
|
OD2
|
E:ASP185
|
3.8
|
13.6
|
1.0
|
|
CA
|
E:CA402
|
3.8
|
13.1
|
1.0
|
|
HB2
|
E:GLU187
|
3.9
|
13.7
|
0.5
|
|
CB
|
E:ASP138
|
4.0
|
8.8
|
1.0
|
|
H
|
E:GLU190
|
4.1
|
15.0
|
1.0
|
|
O
|
E:ASP185
|
4.1
|
12.8
|
1.0
|
|
N
|
E:GLU187
|
4.2
|
13.9
|
0.5
|
|
N
|
E:GLU187
|
4.2
|
13.5
|
0.6
|
|
N
|
E:ILE188
|
4.2
|
11.5
|
1.0
|
|
H
|
E:ASP185
|
4.2
|
16.8
|
1.0
|
|
HB2
|
E:ASP138
|
4.2
|
10.5
|
1.0
|
|
HD13
|
E:ILE188
|
4.2
|
18.2
|
1.0
|
|
OD1
|
E:ASP138
|
4.3
|
13.7
|
1.0
|
|
CA
|
E:GLU187
|
4.3
|
12.0
|
0.5
|
|
HB2
|
E:GLU187
|
4.3
|
22.2
|
0.6
|
|
CA
|
E:ILE188
|
4.3
|
12.5
|
1.0
|
|
CA
|
E:GLU187
|
4.3
|
14.0
|
0.6
|
|
CG
|
E:GLU190
|
4.3
|
13.7
|
1.0
|
|
CG
|
E:GLU177
|
4.4
|
11.0
|
1.0
|
|
N
|
E:GLY189
|
4.4
|
11.6
|
1.0
|
|
O
|
E:HOH596
|
4.4
|
14.2
|
1.0
|
|
C
|
E:ASP185
|
4.6
|
12.8
|
1.0
|
|
HG3
|
E:GLU190
|
4.6
|
16.4
|
1.0
|
|
CB
|
E:GLU187
|
4.6
|
11.4
|
0.5
|
|
HB2
|
E:GLU177
|
4.7
|
15.0
|
1.0
|
|
CB
|
E:ASP185
|
4.8
|
11.2
|
1.0
|
|
HB3
|
E:GLU177
|
4.8
|
15.0
|
1.0
|
|
N
|
E:ASP185
|
4.8
|
14.0
|
1.0
|
|
C
|
E:ILE188
|
4.8
|
12.4
|
1.0
|
|
HG2
|
E:GLU190
|
4.8
|
16.4
|
1.0
|
|
HG2
|
E:GLU177
|
4.8
|
13.2
|
1.0
|
|
CB
|
E:GLU187
|
4.9
|
18.5
|
0.6
|
|
CB
|
E:GLU177
|
4.9
|
12.5
|
1.0
|
|
HG3
|
E:GLU177
|
4.9
|
13.2
|
1.0
|
|
HA
|
E:THR174
|
4.9
|
12.2
|
1.0
|
|
O
|
E:HOH534
|
4.9
|
14.8
|
1.0
|
|
N
|
E:GLU190
|
5.0
|
12.5
|
1.0
|
|
HB3
|
E:GLU190
|
5.0
|
15.4
|
1.0
|
|
H
|
E:ILE188
|
5.0
|
13.8
|
0.5
|
|
CA
|
E:ASP185
|
5.0
|
12.4
|
1.0
|
|
H
|
E:ILE188
|
5.0
|
13.8
|
0.6
|
|
Calcium binding site 4 out
of 4 in 6sbk
Go back to
Calcium Binding Sites List in 6sbk
Calcium binding site 4 out
of 4 in the Thermolysin in Complex with Fragment J13
 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 Fragment J13 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca405
b:11.3
occ:1.00
|
O
|
E:GLN61
|
2.3
|
11.2
|
1.0
|
|
OD1
|
E:ASP57
|
2.4
|
11.3
|
1.0
|
|
O
|
E:HOH711
|
2.4
|
13.5
|
1.0
|
|
O
|
E:HOH542
|
2.4
|
14.2
|
1.0
|
|
OD2
|
E:ASP59
|
2.4
|
11.0
|
1.0
|
|
O
|
E:HOH582
|
2.4
|
12.9
|
1.0
|
|
OD2
|
E:ASP57
|
2.5
|
10.7
|
1.0
|
|
CG
|
E:ASP57
|
2.8
|
11.3
|
1.0
|
|
H
|
E:GLN61
|
3.3
|
13.0
|
1.0
|
|
CG
|
E:ASP59
|
3.3
|
15.9
|
1.0
|
|
C
|
E:GLN61
|
3.4
|
10.0
|
1.0
|
|
H
|
E:ASP59
|
3.6
|
12.7
|
1.0
|
|
HB2
|
E:GLN61
|
3.7
|
14.6
|
1.0
|
|
OD1
|
E:ASP59
|
3.8
|
15.9
|
1.0
|
|
O
|
E:HOH642
|
3.9
|
17.2
|
1.0
|
|
N
|
E:GLN61
|
4.0
|
10.8
|
1.0
|
|
HA
|
E:PHE62
|
4.0
|
12.2
|
1.0
|
|
CA
|
E:GLN61
|
4.2
|
9.9
|
1.0
|
|
H
|
E:ALA58
|
4.2
|
14.6
|
1.0
|
|
CB
|
E:ASP57
|
4.3
|
10.7
|
1.0
|
|
N
|
E:ASP59
|
4.3
|
10.6
|
1.0
|
|
H
|
E:ASN60
|
4.4
|
12.5
|
1.0
|
|
CB
|
E:GLN61
|
4.4
|
12.2
|
1.0
|
|
O
|
E:HOH673
|
4.5
|
14.1
|
1.0
|
|
N
|
E:PHE62
|
4.5
|
10.2
|
1.0
|
|
O
|
E:HOH755
|
4.6
|
19.2
|
1.0
|
|
CB
|
E:ASP59
|
4.6
|
12.3
|
1.0
|
|
O
|
E:HOH529
|
4.6
|
10.9
|
1.0
|
|
OD2
|
E:ASP67
|
4.6
|
11.1
|
1.0
|
|
N
|
E:ASN60
|
4.7
|
10.4
|
1.0
|
|
HB2
|
E:ASP57
|
4.7
|
12.8
|
1.0
|
|
O
|
E:HOH761
|
4.7
|
32.2
|
1.0
|
|
N
|
E:ALA58
|
4.7
|
12.2
|
1.0
|
|
CA
|
E:PHE62
|
4.7
|
10.1
|
1.0
|
|
HB3
|
E:ASP57
|
4.7
|
12.8
|
1.0
|
|
H
|
E:PHE63
|
4.8
|
14.3
|
1.0
|
|
CA
|
E:ASP59
|
4.8
|
9.3
|
1.0
|
|
HB3
|
E:GLN61
|
4.9
|
14.6
|
1.0
|
|
O
|
E:HOH751
|
4.9
|
29.3
|
1.0
|
|
HA
|
E:ASP57
|
4.9
|
12.1
|
1.0
|
|
C
|
E:ASP59
|
4.9
|
11.5
|
1.0
|
|
HB3
|
E:ASP59
|
5.0
|
14.8
|
1.0
|
|
Reference:
F.Magari,
A.Heine,
G.Klebe.
Thermolysin in Complex with Fragment J13 To Be Published.
Page generated: Wed Jul 9 17:46:43 2025
|
