Calcium in PDB 6sc3: Thermolysin in Complex with Fragment J62
Enzymatic activity of Thermolysin in Complex with Fragment J62
All present enzymatic activity of Thermolysin in Complex with Fragment J62:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with Fragment J62, PDB code: 6sc3
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)
|
46.38 /
1.82
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.760,
92.760,
129.004,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
16.4 /
20.5
|
Other elements in 6sc3:
The structure of Thermolysin in Complex with Fragment J62 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin in Complex with Fragment J62
(pdb code 6sc3). 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 J62, PDB code: 6sc3:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6sc3
Go back to
Calcium Binding Sites List in 6sc3
Calcium binding site 1 out
of 4 in the Thermolysin in Complex with Fragment J62
 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 J62 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca401
b:18.3
occ:1.00
|
O
|
E:GLU187
|
2.3
|
19.6
|
1.0
|
|
OD2
|
E:ASP138
|
2.4
|
18.0
|
1.0
|
|
OD1
|
E:ASP185
|
2.4
|
16.7
|
1.0
|
|
OE2
|
E:GLU190
|
2.5
|
19.9
|
1.0
|
|
OE1
|
E:GLU177
|
2.5
|
19.7
|
1.0
|
|
O
|
E:HOH570
|
2.5
|
18.1
|
1.0
|
|
OE1
|
E:GLU190
|
2.5
|
17.7
|
1.0
|
|
OE2
|
E:GLU177
|
2.8
|
18.9
|
1.0
|
|
CD
|
E:GLU190
|
2.8
|
19.4
|
1.0
|
|
CD
|
E:GLU177
|
2.9
|
22.0
|
1.0
|
|
C
|
E:GLU187
|
3.4
|
20.3
|
1.0
|
|
CG
|
E:ASP138
|
3.4
|
24.5
|
1.0
|
|
CG
|
E:ASP185
|
3.4
|
18.3
|
1.0
|
|
HA
|
E:ILE188
|
3.6
|
21.3
|
1.0
|
|
HB3
|
E:ASP138
|
3.6
|
19.2
|
1.0
|
|
H
|
E:GLU187
|
3.7
|
29.1
|
1.0
|
|
OD2
|
E:ASP185
|
3.8
|
21.0
|
1.0
|
|
CA
|
E:CA404
|
3.8
|
18.3
|
1.0
|
|
H
|
E:GLY189
|
3.9
|
20.4
|
1.0
|
|
HB2
|
E:GLU187
|
3.9
|
31.0
|
1.0
|
|
CB
|
E:ASP138
|
4.0
|
16.0
|
1.0
|
|
H
|
E:GLU190
|
4.1
|
21.3
|
1.0
|
|
H
|
E:ASP185
|
4.2
|
20.2
|
1.0
|
|
N
|
E:GLU187
|
4.2
|
24.2
|
1.0
|
|
O
|
E:ASP185
|
4.2
|
19.9
|
1.0
|
|
N
|
E:ILE188
|
4.2
|
18.9
|
1.0
|
|
HD13
|
E:ILE188
|
4.2
|
31.9
|
1.0
|
|
CA
|
E:GLU187
|
4.2
|
21.6
|
1.0
|
|
O
|
E:HOH588
|
4.3
|
32.7
|
1.0
|
|
CA
|
E:ILE188
|
4.3
|
17.7
|
1.0
|
|
HB2
|
E:ASP138
|
4.3
|
19.2
|
1.0
|
|
OD1
|
E:ASP138
|
4.3
|
21.3
|
1.0
|
|
CG
|
E:GLU190
|
4.3
|
19.7
|
1.0
|
|
CG
|
E:GLU177
|
4.4
|
18.1
|
1.0
|
|
N
|
E:GLY189
|
4.5
|
17.0
|
1.0
|
|
O
|
E:HOH522
|
4.5
|
20.9
|
1.0
|
|
HG3
|
E:GLU190
|
4.6
|
23.6
|
1.0
|
|
CB
|
E:GLU187
|
4.6
|
25.8
|
1.0
|
|
C
|
E:ASP185
|
4.6
|
22.4
|
1.0
|
|
HB2
|
E:GLU177
|
4.7
|
22.3
|
1.0
|
|
CB
|
E:ASP185
|
4.7
|
19.8
|
1.0
|
|
N
|
E:ASP185
|
4.7
|
16.8
|
1.0
|
|
HG2
|
E:GLU190
|
4.8
|
23.6
|
1.0
|
|
HG2
|
E:GLU177
|
4.8
|
21.8
|
1.0
|
|
C
|
E:ILE188
|
4.8
|
18.9
|
1.0
|
|
HB3
|
E:GLU177
|
4.8
|
22.3
|
1.0
|
|
O
|
E:HOH541
|
4.9
|
24.3
|
1.0
|
|
HB3
|
E:GLU190
|
4.9
|
21.2
|
1.0
|
|
CB
|
E:GLU177
|
4.9
|
18.6
|
1.0
|
|
HA
|
E:THR174
|
4.9
|
19.0
|
1.0
|
|
HG3
|
E:GLU177
|
4.9
|
21.8
|
1.0
|
|
H
|
E:ILE188
|
5.0
|
22.7
|
1.0
|
|
N
|
E:GLU190
|
5.0
|
17.7
|
1.0
|
|
CA
|
E:ASP185
|
5.0
|
18.1
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6sc3
Go back to
Calcium Binding Sites List in 6sc3
Calcium binding site 2 out
of 4 in the Thermolysin in Complex with Fragment J62
 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 J62 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:17.9
occ:1.00
|
O
|
E:GLN61
|
2.3
|
17.6
|
1.0
|
|
O
|
E:HOH655
|
2.3
|
20.7
|
1.0
|
|
OD1
|
E:ASP59
|
2.4
|
18.0
|
1.0
|
|
OD1
|
E:ASP57
|
2.4
|
17.9
|
1.0
|
|
O
|
E:HOH567
|
2.4
|
18.3
|
1.0
|
|
O
|
E:HOH540
|
2.5
|
21.4
|
1.0
|
|
OD2
|
E:ASP57
|
2.5
|
18.6
|
1.0
|
|
CG
|
E:ASP57
|
2.8
|
19.0
|
1.0
|
|
H
|
E:GLN61
|
3.3
|
22.0
|
1.0
|
|
CG
|
E:ASP59
|
3.4
|
26.2
|
1.0
|
|
C
|
E:GLN61
|
3.4
|
18.1
|
1.0
|
|
H
|
E:ASP59
|
3.5
|
22.6
|
1.0
|
|
HB2
|
E:GLN61
|
3.7
|
24.7
|
1.0
|
|
OD2
|
E:ASP59
|
3.8
|
23.0
|
1.0
|
|
N
|
E:GLN61
|
4.0
|
18.3
|
1.0
|
|
HA
|
E:PHE62
|
4.0
|
18.6
|
1.0
|
|
O
|
E:HOH610
|
4.0
|
25.3
|
1.0
|
|
CA
|
E:GLN61
|
4.1
|
17.5
|
1.0
|
|
H
|
E:ALA58
|
4.3
|
22.7
|
1.0
|
|
CB
|
E:ASP57
|
4.3
|
14.8
|
1.0
|
|
N
|
E:ASP59
|
4.3
|
18.8
|
1.0
|
|
CB
|
E:GLN61
|
4.4
|
20.5
|
1.0
|
|
H
|
E:ASN60
|
4.4
|
21.2
|
1.0
|
|
O
|
E:HOH642
|
4.5
|
17.1
|
1.0
|
|
N
|
E:PHE62
|
4.5
|
16.8
|
1.0
|
|
O
|
E:HOH509
|
4.6
|
15.1
|
1.0
|
|
CB
|
E:ASP59
|
4.6
|
20.0
|
1.0
|
|
OD2
|
E:ASP67
|
4.7
|
18.0
|
1.0
|
|
O
|
E:HOH688
|
4.7
|
34.8
|
1.0
|
|
N
|
E:ASN60
|
4.7
|
17.6
|
1.0
|
|
HB2
|
E:ASP57
|
4.7
|
17.8
|
1.0
|
|
HB3
|
E:ASP57
|
4.7
|
17.8
|
1.0
|
|
N
|
E:ALA58
|
4.7
|
18.9
|
1.0
|
|
H
|
E:PHE63
|
4.7
|
20.2
|
1.0
|
|
CA
|
E:PHE62
|
4.8
|
15.4
|
1.0
|
|
CA
|
E:ASP59
|
4.8
|
17.9
|
1.0
|
|
HB3
|
E:GLN61
|
4.8
|
24.7
|
1.0
|
|
HA
|
E:ASP57
|
4.8
|
21.1
|
1.0
|
|
C
|
E:ASP59
|
4.9
|
20.9
|
1.0
|
|
HB3
|
E:ASP59
|
4.9
|
24.0
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6sc3
Go back to
Calcium Binding Sites List in 6sc3
Calcium binding site 3 out
of 4 in the Thermolysin in Complex with Fragment J62
 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 J62 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:22.4
occ:1.00
|
O
|
E:ILE197
|
2.3
|
29.1
|
1.0
|
|
O
|
E:HOH647
|
2.3
|
30.5
|
1.0
|
|
O
|
E:TYR193
|
2.4
|
19.9
|
1.0
|
|
OG1
|
E:THR194
|
2.4
|
24.1
|
1.0
|
|
OD1
|
E:ASP200
|
2.4
|
24.1
|
1.0
|
|
O
|
E:THR194
|
2.4
|
25.9
|
1.0
|
|
O
|
E:HOH518
|
2.5
|
23.7
|
1.0
|
|
C
|
E:THR194
|
3.3
|
24.7
|
1.0
|
|
C
|
E:TYR193
|
3.3
|
26.5
|
1.0
|
|
C
|
E:ILE197
|
3.5
|
33.5
|
1.0
|
|
HB
|
E:ILE197
|
3.5
|
41.5
|
1.0
|
|
CB
|
E:THR194
|
3.5
|
21.6
|
1.0
|
|
CG
|
E:ASP200
|
3.5
|
26.2
|
1.0
|
|
H
|
E:ILE197
|
3.6
|
43.9
|
1.0
|
|
CA
|
E:THR194
|
3.7
|
25.6
|
1.0
|
|
HB
|
E:THR194
|
3.7
|
25.9
|
1.0
|
|
H
|
E:ASP200
|
3.8
|
33.7
|
1.0
|
|
OD2
|
E:ASP200
|
3.9
|
24.5
|
1.0
|
|
N
|
E:THR194
|
3.9
|
20.5
|
1.0
|
|
HA
|
E:SER198
|
4.1
|
34.2
|
1.0
|
|
HB3
|
E:TYR193
|
4.1
|
23.5
|
1.0
|
|
HD2
|
E:TYR193
|
4.2
|
29.9
|
1.0
|
|
CA
|
E:ILE197
|
4.2
|
28.0
|
1.0
|
|
N
|
E:ILE197
|
4.2
|
36.5
|
1.0
|
|
CB
|
E:ILE197
|
4.2
|
34.5
|
1.0
|
|
N
|
E:PRO195
|
4.4
|
23.1
|
1.0
|
|
HA
|
E:PRO195
|
4.4
|
34.9
|
1.0
|
|
O
|
E:ASP200
|
4.4
|
20.6
|
1.0
|
|
N
|
E:SER198
|
4.5
|
30.3
|
1.0
|
|
CA
|
E:TYR193
|
4.5
|
18.1
|
1.0
|
|
HG22
|
E:ILE197
|
4.5
|
37.6
|
1.0
|
|
N
|
E:ASP200
|
4.6
|
28.0
|
1.0
|
|
CA
|
E:SER198
|
4.6
|
28.5
|
1.0
|
|
HA
|
E:THR194
|
4.7
|
30.7
|
1.0
|
|
O
|
E:GLU190
|
4.7
|
18.3
|
1.0
|
|
H
|
E:THR194
|
4.7
|
24.6
|
1.0
|
|
CG2
|
E:THR194
|
4.7
|
22.3
|
1.0
|
|
CB
|
E:TYR193
|
4.7
|
19.6
|
1.0
|
|
H
|
E:GLY199
|
4.7
|
32.9
|
1.0
|
|
CD2
|
E:TYR193
|
4.7
|
24.9
|
1.0
|
|
CA
|
E:PRO195
|
4.7
|
29.0
|
1.0
|
|
CB
|
E:ASP200
|
4.8
|
26.2
|
1.0
|
|
C
|
E:ASP200
|
4.8
|
23.4
|
1.0
|
|
HG23
|
E:THR194
|
4.8
|
26.7
|
1.0
|
|
H
|
E:TYR193
|
4.9
|
20.9
|
1.0
|
|
CG2
|
E:ILE197
|
4.9
|
31.3
|
1.0
|
|
C
|
E:SER198
|
4.9
|
29.9
|
1.0
|
|
HG21
|
E:THR194
|
5.0
|
26.7
|
1.0
|
|
N
|
E:GLY199
|
5.0
|
27.4
|
1.0
|
|
C
|
E:PRO195
|
5.0
|
30.3
|
1.0
|
|
CA
|
E:ASP200
|
5.0
|
20.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6sc3
Go back to
Calcium Binding Sites List in 6sc3
Calcium binding site 4 out
of 4 in the Thermolysin in Complex with Fragment J62
 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 J62 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca404
b:18.3
occ:1.00
|
O
|
E:HOH541
|
2.2
|
24.3
|
1.0
|
|
OE2
|
E:GLU190
|
2.3
|
19.9
|
1.0
|
|
O
|
E:ASN183
|
2.3
|
25.6
|
1.0
|
|
O
|
E:HOH613
|
2.3
|
24.2
|
1.0
|
|
OE2
|
E:GLU177
|
2.4
|
18.9
|
1.0
|
|
OD2
|
E:ASP185
|
2.4
|
21.0
|
1.0
|
|
CD
|
E:GLU177
|
3.3
|
22.0
|
1.0
|
|
CG
|
E:ASP185
|
3.3
|
18.3
|
1.0
|
|
CD
|
E:GLU190
|
3.3
|
19.4
|
1.0
|
|
C
|
E:ASN183
|
3.5
|
18.3
|
1.0
|
|
HG3
|
E:GLU190
|
3.6
|
23.6
|
1.0
|
|
HA
|
E:PRO184
|
3.6
|
23.3
|
1.0
|
|
OD1
|
E:ASP185
|
3.7
|
16.7
|
1.0
|
|
HG2
|
E:GLU190
|
3.7
|
23.6
|
1.0
|
|
CG
|
E:GLU190
|
3.8
|
19.7
|
1.0
|
|
CA
|
E:CA401
|
3.8
|
18.3
|
1.0
|
|
HB2
|
E:ASN183
|
3.8
|
28.4
|
1.0
|
|
HB3
|
E:ASN183
|
3.8
|
28.4
|
1.0
|
|
OE1
|
E:GLU177
|
3.9
|
19.7
|
1.0
|
|
H
|
E:ASP185
|
4.1
|
20.2
|
1.0
|
|
OD2
|
E:ASP191
|
4.1
|
20.7
|
1.0
|
|
CA
|
E:PRO184
|
4.1
|
19.4
|
1.0
|
|
CB
|
E:ASN183
|
4.2
|
23.7
|
1.0
|
|
N
|
E:ASP185
|
4.2
|
16.8
|
1.0
|
|
OD1
|
E:ASP191
|
4.2
|
24.5
|
1.0
|
|
CG
|
E:GLU177
|
4.3
|
18.1
|
1.0
|
|
N
|
E:PRO184
|
4.3
|
19.8
|
1.0
|
|
C
|
E:PRO184
|
4.3
|
22.9
|
1.0
|
|
HG2
|
E:GLU177
|
4.3
|
21.8
|
1.0
|
|
OE1
|
E:GLU190
|
4.3
|
17.7
|
1.0
|
|
HG3
|
E:GLU177
|
4.3
|
21.8
|
1.0
|
|
O
|
E:LYS182
|
4.4
|
26.3
|
1.0
|
|
HB3
|
E:ASP185
|
4.4
|
23.8
|
1.0
|
|
CB
|
E:ASP185
|
4.4
|
19.8
|
1.0
|
|
O
|
E:HOH588
|
4.5
|
32.7
|
1.0
|
|
CA
|
E:ASN183
|
4.5
|
22.6
|
1.0
|
|
CG
|
E:ASP191
|
4.5
|
24.5
|
1.0
|
|
O
|
E:PRO184
|
4.9
|
26.8
|
1.0
|
|
CA
|
E:ASP185
|
5.0
|
18.1
|
1.0
|
|
Reference:
F.Magari,
A.Heine,
G.Klebe.
Thermolysin in Complex with Fragment J62 To Be Published.
Page generated: Tue Jul 16 14:43:38 2024
|
