Calcium in PDB 5jxn: Thermolysin in Complex with JC240.
Enzymatic activity of Thermolysin in Complex with JC240.
All present enzymatic activity of Thermolysin in Complex with JC240.:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with JC240., PDB code: 5jxn
was solved by
S.G.Krimmer,
J.Cramer,
A.Heine,
G.Klebe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.51 /
1.38
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.014,
93.014,
131.203,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
11 /
13.5
|
Other elements in 5jxn:
The structure of Thermolysin in Complex with JC240. also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin in Complex with JC240.
(pdb code 5jxn). 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 JC240., PDB code: 5jxn:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5jxn
Go back to
Calcium Binding Sites List in 5jxn
Calcium binding site 1 out
of 4 in the Thermolysin in Complex with JC240.
 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 JC240. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:10.4
occ:1.00
|
O
|
E:GLU187
|
2.3
|
10.9
|
1.0
|
|
OD2
|
E:ASP138
|
2.4
|
10.4
|
1.0
|
|
O
|
E:HOH610
|
2.4
|
10.3
|
1.0
|
|
OE1
|
E:GLU190
|
2.5
|
10.8
|
1.0
|
|
OE1
|
E:GLU177
|
2.5
|
11.2
|
1.0
|
|
OE2
|
E:GLU190
|
2.5
|
12.2
|
1.0
|
|
OD1
|
E:ASP185
|
2.5
|
10.7
|
1.0
|
|
OE2
|
E:GLU177
|
2.7
|
12.0
|
1.0
|
|
CD
|
E:GLU190
|
2.8
|
11.1
|
1.0
|
|
CD
|
E:GLU177
|
2.9
|
10.6
|
1.0
|
|
CG
|
E:ASP138
|
3.4
|
10.3
|
1.0
|
|
C
|
E:GLU187
|
3.4
|
11.2
|
1.0
|
|
CG
|
E:ASP185
|
3.5
|
11.8
|
1.0
|
|
HB3
|
E:ASP138
|
3.6
|
11.1
|
1.0
|
|
HA
|
E:ILE188
|
3.7
|
11.9
|
1.0
|
|
H
|
E:GLU187
|
3.8
|
13.1
|
1.0
|
|
H
|
E:GLY189
|
3.8
|
12.8
|
1.0
|
|
CA
|
E:CA404
|
3.8
|
14.1
|
1.0
|
|
OD2
|
E:ASP185
|
3.8
|
14.1
|
1.0
|
|
HB2
|
E:GLU187
|
3.9
|
15.9
|
1.0
|
|
CB
|
E:ASP138
|
4.0
|
9.2
|
1.0
|
|
O
|
E:ASP185
|
4.2
|
11.3
|
1.0
|
|
H
|
E:ASP185
|
4.2
|
14.5
|
1.0
|
|
H
|
E:GLU190
|
4.2
|
13.2
|
1.0
|
|
N
|
E:GLU187
|
4.2
|
10.9
|
1.0
|
|
N
|
E:ILE188
|
4.2
|
10.2
|
1.0
|
|
HB2
|
E:ASP138
|
4.3
|
11.1
|
1.0
|
|
CA
|
E:GLU187
|
4.3
|
11.5
|
1.0
|
|
OD1
|
E:ASP138
|
4.3
|
11.2
|
1.0
|
|
CA
|
E:ILE188
|
4.3
|
9.9
|
1.0
|
|
CG
|
E:GLU190
|
4.4
|
12.1
|
1.0
|
|
HD13
|
E:ILE188
|
4.4
|
16.0
|
1.0
|
|
CG
|
E:GLU177
|
4.4
|
10.6
|
1.0
|
|
N
|
E:GLY189
|
4.4
|
10.7
|
1.0
|
|
O
|
E:HOH563
|
4.5
|
16.2
|
1.0
|
|
CB
|
E:GLU187
|
4.6
|
13.3
|
1.0
|
|
C
|
E:ASP185
|
4.6
|
11.6
|
1.0
|
|
HG3
|
E:GLU190
|
4.6
|
14.6
|
1.0
|
|
HB2
|
E:GLU177
|
4.7
|
12.4
|
1.0
|
|
HB3
|
E:GLU177
|
4.7
|
12.4
|
1.0
|
|
C
|
E:ILE188
|
4.8
|
10.4
|
1.0
|
|
N
|
E:ASP185
|
4.8
|
12.1
|
1.0
|
|
CB
|
E:ASP185
|
4.8
|
11.6
|
1.0
|
|
HG2
|
E:GLU190
|
4.8
|
14.6
|
1.0
|
|
HG2
|
E:GLU177
|
4.8
|
12.7
|
1.0
|
|
O
|
E:HOH580
|
4.9
|
17.3
|
1.0
|
|
CB
|
E:GLU177
|
4.9
|
10.3
|
1.0
|
|
HA
|
E:THR174
|
4.9
|
11.4
|
1.0
|
|
HG3
|
E:GLU177
|
4.9
|
12.7
|
1.0
|
|
N
|
E:GLU190
|
5.0
|
11.0
|
1.0
|
|
HB3
|
E:GLU190
|
5.0
|
14.5
|
1.0
|
|
CA
|
E:ASP185
|
5.0
|
11.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5jxn
Go back to
Calcium Binding Sites List in 5jxn
Calcium binding site 2 out
of 4 in the Thermolysin in Complex with JC240.
 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 JC240. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:11.1
occ:1.00
|
O
|
E:GLN61
|
2.2
|
11.0
|
1.0
|
|
O
|
E:HOH783
|
2.3
|
13.1
|
1.0
|
|
OD1
|
E:ASP57
|
2.4
|
11.4
|
1.0
|
|
OD1
|
E:ASP59
|
2.4
|
11.3
|
1.0
|
|
O
|
E:HOH605
|
2.4
|
13.6
|
1.0
|
|
O
|
E:HOH582
|
2.4
|
12.8
|
1.0
|
|
OD2
|
E:ASP57
|
2.6
|
11.4
|
1.0
|
|
CG
|
E:ASP57
|
2.8
|
10.5
|
1.0
|
|
H
|
E:GLN61
|
3.3
|
12.9
|
1.0
|
|
CG
|
E:ASP59
|
3.4
|
12.4
|
1.0
|
|
C
|
E:GLN61
|
3.4
|
10.2
|
1.0
|
|
H
|
E:ASP59
|
3.5
|
13.3
|
1.0
|
|
HB2
|
E:GLN61
|
3.6
|
17.1
|
1.0
|
|
OD2
|
E:ASP59
|
3.8
|
14.9
|
1.0
|
|
N
|
E:GLN61
|
4.0
|
10.8
|
1.0
|
|
O
|
E:HOH707
|
4.0
|
18.7
|
1.0
|
|
HA
|
E:PHE62
|
4.0
|
12.1
|
1.0
|
|
CA
|
E:GLN61
|
4.1
|
11.8
|
1.0
|
|
H
|
E:ALA58
|
4.3
|
12.8
|
1.0
|
|
CB
|
E:GLN61
|
4.3
|
14.2
|
1.0
|
|
N
|
E:ASP59
|
4.3
|
11.1
|
1.0
|
|
CB
|
E:ASP57
|
4.3
|
10.6
|
1.0
|
|
H
|
E:ASN60
|
4.4
|
12.4
|
1.0
|
|
N
|
E:PHE62
|
4.5
|
9.8
|
1.0
|
|
CB
|
E:ASP59
|
4.6
|
11.7
|
1.0
|
|
OD2
|
E:ASP67
|
4.7
|
10.7
|
1.0
|
|
O
|
E:HOH531
|
4.7
|
10.8
|
1.0
|
|
N
|
E:ASN60
|
4.7
|
10.3
|
1.0
|
|
O
|
E:HOH891
|
4.7
|
30.0
|
1.0
|
|
HB2
|
E:ASP57
|
4.7
|
12.8
|
1.0
|
|
N
|
E:ALA58
|
4.7
|
10.7
|
1.0
|
|
CA
|
E:PHE62
|
4.8
|
10.1
|
1.0
|
|
HB3
|
E:ASP57
|
4.8
|
12.8
|
1.0
|
|
CA
|
E:ASP59
|
4.8
|
11.0
|
1.0
|
|
HA
|
E:ASP57
|
4.9
|
12.2
|
1.0
|
|
H
|
E:PHE63
|
4.9
|
13.6
|
1.0
|
|
C
|
E:ASP59
|
4.9
|
10.9
|
1.0
|
|
HB3
|
E:GLN61
|
4.9
|
17.1
|
1.0
|
|
HB3
|
E:ASP59
|
5.0
|
14.0
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5jxn
Go back to
Calcium Binding Sites List in 5jxn
Calcium binding site 3 out
of 4 in the Thermolysin in Complex with JC240.
 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 JC240. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca404
b:14.1
occ:1.00
|
OE2
|
E:GLU190
|
2.3
|
12.2
|
1.0
|
|
O
|
E:ASN183
|
2.3
|
15.9
|
1.0
|
|
OD2
|
E:ASP185
|
2.3
|
14.1
|
1.0
|
|
O
|
E:HOH580
|
2.3
|
17.3
|
1.0
|
|
O
|
E:HOH591
|
2.3
|
17.6
|
1.0
|
|
OE2
|
E:GLU177
|
2.4
|
12.0
|
1.0
|
|
CG
|
E:ASP185
|
3.2
|
11.8
|
1.0
|
|
CD
|
E:GLU177
|
3.2
|
10.6
|
1.0
|
|
CD
|
E:GLU190
|
3.3
|
11.1
|
1.0
|
|
C
|
E:ASN183
|
3.5
|
15.8
|
1.0
|
|
HA
|
E:PRO184
|
3.5
|
15.9
|
1.0
|
|
HG3
|
E:GLU190
|
3.6
|
14.6
|
1.0
|
|
OD1
|
E:ASP185
|
3.6
|
10.7
|
1.0
|
|
OE1
|
E:GLU177
|
3.7
|
11.2
|
1.0
|
|
CA
|
E:CA402
|
3.8
|
10.4
|
1.0
|
|
HB3
|
E:ASN183
|
3.8
|
24.7
|
1.0
|
|
HG2
|
E:GLU190
|
3.8
|
14.6
|
1.0
|
|
HB2
|
E:ASN183
|
3.8
|
24.7
|
1.0
|
|
CG
|
E:GLU190
|
3.8
|
12.1
|
1.0
|
|
H
|
E:ASP185
|
4.0
|
14.5
|
1.0
|
|
CA
|
E:PRO184
|
4.1
|
13.2
|
1.0
|
|
N
|
E:ASP185
|
4.2
|
12.1
|
1.0
|
|
CB
|
E:ASN183
|
4.2
|
20.6
|
1.0
|
|
OD1
|
E:ASP191
|
4.3
|
16.1
|
1.0
|
|
OD2
|
E:ASP191
|
4.3
|
15.2
|
1.0
|
|
CG
|
E:GLU177
|
4.3
|
10.6
|
1.0
|
|
HG2
|
E:GLU177
|
4.3
|
12.7
|
1.0
|
|
OE1
|
E:GLU190
|
4.3
|
10.8
|
1.0
|
|
C
|
E:PRO184
|
4.3
|
13.7
|
1.0
|
|
N
|
E:PRO184
|
4.3
|
14.1
|
1.0
|
|
HB3
|
E:ASP185
|
4.3
|
13.9
|
1.0
|
|
HG3
|
E:GLU177
|
4.4
|
12.7
|
1.0
|
|
CB
|
E:ASP185
|
4.4
|
11.6
|
1.0
|
|
O
|
E:LYS182
|
4.4
|
19.2
|
1.0
|
|
O
|
E:HOH540
|
4.4
|
42.0
|
1.0
|
|
CA
|
E:ASN183
|
4.5
|
17.8
|
1.0
|
|
CG
|
E:ASP191
|
4.6
|
14.8
|
1.0
|
|
O
|
E:HOH861
|
4.7
|
41.4
|
1.0
|
|
CA
|
E:ASP185
|
4.9
|
11.8
|
1.0
|
|
O
|
E:PRO184
|
5.0
|
15.6
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5jxn
Go back to
Calcium Binding Sites List in 5jxn
Calcium binding site 4 out
of 4 in the Thermolysin in Complex with JC240.
 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 JC240. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca405
b:14.2
occ:1.00
|
O
|
E:ILE197
|
2.3
|
20.0
|
1.0
|
|
OG1
|
E:THR194
|
2.4
|
14.7
|
1.0
|
|
O
|
E:THR194
|
2.4
|
15.7
|
1.0
|
|
OD1
|
E:ASP200
|
2.4
|
14.9
|
1.0
|
|
O
|
E:TYR193
|
2.4
|
13.6
|
1.0
|
|
O
|
E:HOH554
|
2.4
|
16.4
|
1.0
|
|
O
|
E:HOH774
|
2.4
|
22.1
|
1.0
|
|
C
|
E:THR194
|
3.2
|
15.2
|
1.0
|
|
C
|
E:TYR193
|
3.4
|
13.7
|
1.0
|
|
CG
|
E:ASP200
|
3.4
|
14.6
|
1.0
|
|
CB
|
E:THR194
|
3.4
|
14.6
|
1.0
|
|
C
|
E:ILE197
|
3.5
|
21.1
|
1.0
|
|
HB
|
E:ILE197
|
3.5
|
27.5
|
1.0
|
|
CA
|
E:THR194
|
3.6
|
14.1
|
1.0
|
|
H
|
E:ILE197
|
3.6
|
26.2
|
1.0
|
|
HB
|
E:THR194
|
3.7
|
17.6
|
1.0
|
|
OD2
|
E:ASP200
|
3.8
|
16.2
|
1.0
|
|
N
|
E:THR194
|
3.9
|
13.6
|
1.0
|
|
H
|
E:ASP200
|
3.9
|
20.5
|
1.0
|
|
HD2
|
E:TYR193
|
4.0
|
17.6
|
1.0
|
|
HB3
|
E:TYR193
|
4.0
|
15.9
|
1.0
|
|
HA
|
E:SER198
|
4.2
|
29.3
|
1.0
|
|
CA
|
E:ILE197
|
4.2
|
22.1
|
1.0
|
|
N
|
E:PRO195
|
4.3
|
15.9
|
1.0
|
|
CB
|
E:ILE197
|
4.3
|
22.9
|
1.0
|
|
HA
|
E:PRO195
|
4.3
|
20.8
|
1.0
|
|
N
|
E:ILE197
|
4.3
|
21.8
|
1.0
|
|
HG22
|
E:ILE197
|
4.4
|
26.8
|
1.0
|
|
O
|
E:ASP200
|
4.5
|
15.1
|
1.0
|
|
N
|
E:SER198
|
4.5
|
22.9
|
1.0
|
|
HA
|
E:THR194
|
4.6
|
16.9
|
1.0
|
|
O
|
E:HOH761
|
4.6
|
46.0
|
1.0
|
|
CA
|
E:TYR193
|
4.6
|
12.8
|
1.0
|
|
O
|
E:HOH753
|
4.6
|
38.6
|
1.0
|
|
CD2
|
E:TYR193
|
4.6
|
14.7
|
1.0
|
|
O
|
E:HOH787
|
4.6
|
27.6
|
1.0
|
|
CA
|
E:PRO195
|
4.7
|
17.4
|
1.0
|
|
O
|
E:GLU190
|
4.7
|
13.1
|
1.0
|
|
CB
|
E:TYR193
|
4.7
|
13.2
|
1.0
|
|
N
|
E:ASP200
|
4.7
|
17.1
|
1.0
|
|
CA
|
E:SER198
|
4.7
|
24.4
|
1.0
|
|
H
|
E:THR194
|
4.7
|
16.4
|
1.0
|
|
CB
|
E:ASP200
|
4.7
|
15.6
|
1.0
|
|
CG2
|
E:THR194
|
4.7
|
15.2
|
1.0
|
|
H
|
E:GLY199
|
4.8
|
24.9
|
1.0
|
|
C
|
E:ASP200
|
4.8
|
15.3
|
1.0
|
|
CG2
|
E:ILE197
|
4.9
|
22.4
|
1.0
|
|
HG23
|
E:THR194
|
4.9
|
18.3
|
1.0
|
|
H
|
E:TYR193
|
4.9
|
14.4
|
1.0
|
|
C
|
E:PRO195
|
4.9
|
20.1
|
1.0
|
|
C
|
E:SER198
|
5.0
|
23.4
|
1.0
|
|
CA
|
E:ASP200
|
5.0
|
15.8
|
1.0
|
|
HG21
|
E:THR194
|
5.0
|
18.3
|
1.0
|
|
Reference:
S.G.Krimmer,
J.Cramer,
M.Betz,
V.Fridh,
R.Karlsson,
A.Heine,
G.Klebe.
Rational Design of Thermodynamic and Kinetic Binding Profiles By Optimizing Surface Water Networks Coating Protein-Bound Ligands. J. Med. Chem. V. 59 10530 2016.
ISSN: ISSN 1520-4804
PubMed: 27933956
DOI: 10.1021/ACS.JMEDCHEM.6B00998
Page generated: Wed Jul 9 07:15:08 2025
|
