Calcium in PDB 5n2t: Thermolysin in Complex with Inhibitor JC287
Enzymatic activity of Thermolysin in Complex with Inhibitor JC287
All present enzymatic activity of Thermolysin in Complex with Inhibitor JC287:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with Inhibitor JC287, PDB code: 5n2t
was solved by
J.Cramer,
S.G.Krimmer,
A.Heine,
G.Klebe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.52 /
1.38
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.047,
93.047,
130.795,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
11.2 /
13.8
|
Other elements in 5n2t:
The structure of Thermolysin in Complex with Inhibitor JC287 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin in Complex with Inhibitor JC287
(pdb code 5n2t). 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 Inhibitor JC287, PDB code: 5n2t:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5n2t
Go back to
Calcium Binding Sites List in 5n2t
Calcium binding site 1 out
of 4 in the Thermolysin in Complex with Inhibitor JC287
 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 Inhibitor JC287 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:10.2
occ:1.00
|
O
|
E:GLN61
|
2.3
|
10.8
|
1.0
|
|
O
|
E:HOH771
|
2.3
|
12.5
|
1.0
|
|
OD2
|
E:ASP57
|
2.4
|
10.5
|
1.0
|
|
O
|
E:HOH590
|
2.4
|
12.6
|
1.0
|
|
OD1
|
E:ASP59
|
2.4
|
10.8
|
1.0
|
|
O
|
E:HOH603
|
2.4
|
11.7
|
1.0
|
|
OD1
|
E:ASP57
|
2.6
|
10.1
|
1.0
|
|
CG
|
E:ASP57
|
2.8
|
9.8
|
1.0
|
|
H
|
E:GLN61
|
3.3
|
12.6
|
1.0
|
|
CG
|
E:ASP59
|
3.4
|
11.3
|
1.0
|
|
C
|
E:GLN61
|
3.4
|
10.2
|
1.0
|
|
H
|
E:ASP59
|
3.5
|
12.7
|
1.0
|
|
HB2
|
E:GLN61
|
3.7
|
17.3
|
1.0
|
|
OD2
|
E:ASP59
|
3.8
|
14.5
|
1.0
|
|
N
|
E:GLN61
|
4.0
|
10.5
|
1.0
|
|
O
|
E:HOH695
|
4.0
|
17.0
|
1.0
|
|
HA
|
E:PHE62
|
4.0
|
11.7
|
1.0
|
|
CA
|
E:GLN61
|
4.2
|
10.9
|
1.0
|
|
H
|
E:ALA58
|
4.3
|
12.1
|
1.0
|
|
N
|
E:ASP59
|
4.3
|
10.6
|
1.0
|
|
CB
|
E:ASP57
|
4.3
|
10.0
|
1.0
|
|
H
|
E:ASN60
|
4.3
|
11.8
|
1.0
|
|
CB
|
E:GLN61
|
4.4
|
14.4
|
1.0
|
|
O
|
E:HOH731
|
4.5
|
13.1
|
1.0
|
|
N
|
E:PHE62
|
4.5
|
9.5
|
1.0
|
|
O
|
E:HOH835
|
4.6
|
15.5
|
1.0
|
|
CB
|
E:ASP59
|
4.6
|
10.9
|
1.0
|
|
OD2
|
E:ASP67
|
4.6
|
9.7
|
1.0
|
|
N
|
E:ASN60
|
4.7
|
9.9
|
1.0
|
|
O
|
E:HOH533
|
4.7
|
10.0
|
1.0
|
|
O
|
E:HOH847
|
4.7
|
24.1
|
1.0
|
|
HB2
|
E:ASP57
|
4.7
|
11.9
|
1.0
|
|
N
|
E:ALA58
|
4.7
|
10.1
|
1.0
|
|
CA
|
E:PHE62
|
4.8
|
9.7
|
1.0
|
|
O
|
E:HOH827
|
4.8
|
28.5
|
1.0
|
|
HB3
|
E:ASP57
|
4.8
|
11.9
|
1.0
|
|
CA
|
E:ASP59
|
4.8
|
10.4
|
1.0
|
|
H
|
E:PHE63
|
4.9
|
12.7
|
1.0
|
|
HA
|
E:ASP57
|
4.9
|
12.2
|
1.0
|
|
C
|
E:ASP59
|
4.9
|
10.3
|
1.0
|
|
HB3
|
E:GLN61
|
5.0
|
17.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5n2t
Go back to
Calcium Binding Sites List in 5n2t
Calcium binding site 2 out
of 4 in the Thermolysin in Complex with Inhibitor JC287
 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 Inhibitor JC287 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:9.7
occ:1.00
|
O
|
E:GLU187
|
2.3
|
10.6
|
1.0
|
|
OD2
|
E:ASP138
|
2.4
|
9.5
|
1.0
|
|
O
|
E:HOH553
|
2.5
|
10.4
|
1.0
|
|
OE1
|
E:GLU177
|
2.5
|
10.6
|
1.0
|
|
OE1
|
E:GLU190
|
2.5
|
10.6
|
1.0
|
|
OD1
|
E:ASP185
|
2.5
|
10.8
|
1.0
|
|
OE2
|
E:GLU190
|
2.5
|
10.9
|
1.0
|
|
OE2
|
E:GLU177
|
2.7
|
11.1
|
1.0
|
|
CD
|
E:GLU190
|
2.8
|
10.6
|
1.0
|
|
CD
|
E:GLU177
|
2.9
|
9.8
|
1.0
|
|
CG
|
E:ASP138
|
3.4
|
9.1
|
1.0
|
|
C
|
E:GLU187
|
3.4
|
11.2
|
1.0
|
|
CG
|
E:ASP185
|
3.5
|
11.6
|
1.0
|
|
HB3
|
E:ASP138
|
3.6
|
10.6
|
1.0
|
|
HA
|
E:ILE188
|
3.7
|
11.7
|
1.0
|
|
H
|
E:GLU187
|
3.7
|
13.2
|
1.0
|
|
H
|
E:GLY189
|
3.8
|
12.6
|
1.0
|
|
OD2
|
E:ASP185
|
3.8
|
13.3
|
1.0
|
|
CA
|
E:CA404
|
3.8
|
12.9
|
1.0
|
|
HB2
|
E:GLU187
|
3.9
|
17.6
|
1.0
|
|
CB
|
E:ASP138
|
4.0
|
8.8
|
1.0
|
|
H
|
E:GLU190
|
4.1
|
12.7
|
1.0
|
|
H
|
E:ASP185
|
4.2
|
13.5
|
1.0
|
|
O
|
E:ASP185
|
4.2
|
11.2
|
1.0
|
|
N
|
E:GLU187
|
4.2
|
11.0
|
1.0
|
|
OD1
|
E:ASP138
|
4.2
|
10.8
|
1.0
|
|
O
|
E:HOH556
|
4.3
|
33.9
|
1.0
|
|
N
|
E:ILE188
|
4.3
|
10.0
|
1.0
|
|
HB2
|
E:ASP138
|
4.3
|
10.6
|
1.0
|
|
CA
|
E:GLU187
|
4.3
|
11.5
|
1.0
|
|
HD13
|
E:ILE188
|
4.3
|
15.3
|
1.0
|
|
CG
|
E:GLU190
|
4.3
|
11.3
|
1.0
|
|
CA
|
E:ILE188
|
4.3
|
9.7
|
1.0
|
|
N
|
E:GLY189
|
4.4
|
10.5
|
1.0
|
|
CG
|
E:GLU177
|
4.4
|
10.2
|
1.0
|
|
O
|
E:HOH572
|
4.4
|
15.3
|
1.0
|
|
C
|
E:ASP185
|
4.6
|
11.1
|
1.0
|
|
HG3
|
E:GLU190
|
4.6
|
13.5
|
1.0
|
|
CB
|
E:GLU187
|
4.6
|
14.7
|
1.0
|
|
HB2
|
E:GLU177
|
4.7
|
11.7
|
1.0
|
|
HB3
|
E:GLU177
|
4.8
|
11.7
|
1.0
|
|
C
|
E:ILE188
|
4.8
|
10.2
|
1.0
|
|
CB
|
E:ASP185
|
4.8
|
11.5
|
1.0
|
|
N
|
E:ASP185
|
4.8
|
11.3
|
1.0
|
|
HG2
|
E:GLU190
|
4.8
|
13.5
|
1.0
|
|
HG2
|
E:GLU177
|
4.8
|
12.2
|
1.0
|
|
HA
|
E:THR174
|
4.9
|
10.8
|
1.0
|
|
CB
|
E:GLU177
|
4.9
|
9.7
|
1.0
|
|
O
|
E:HOH573
|
4.9
|
15.2
|
1.0
|
|
HG3
|
E:GLU177
|
4.9
|
12.2
|
1.0
|
|
N
|
E:GLU190
|
4.9
|
10.6
|
1.0
|
|
HB3
|
E:GLU190
|
5.0
|
14.0
|
1.0
|
|
CA
|
E:ASP185
|
5.0
|
11.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5n2t
Go back to
Calcium Binding Sites List in 5n2t
Calcium binding site 3 out
of 4 in the Thermolysin in Complex with Inhibitor JC287
 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 Inhibitor JC287 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca404
b:12.9
occ:1.00
|
OE2
|
E:GLU190
|
2.3
|
10.9
|
1.0
|
|
O
|
E:ASN183
|
2.3
|
14.9
|
1.0
|
|
OD2
|
E:ASP185
|
2.3
|
13.3
|
1.0
|
|
O
|
E:HOH573
|
2.3
|
15.2
|
1.0
|
|
O
|
E:HOH561
|
2.3
|
16.4
|
1.0
|
|
OE2
|
E:GLU177
|
2.4
|
11.1
|
1.0
|
|
CG
|
E:ASP185
|
3.2
|
11.6
|
1.0
|
|
CD
|
E:GLU177
|
3.2
|
9.8
|
1.0
|
|
CD
|
E:GLU190
|
3.3
|
10.6
|
1.0
|
|
C
|
E:ASN183
|
3.5
|
15.0
|
1.0
|
|
HA
|
E:PRO184
|
3.6
|
15.4
|
1.0
|
|
HG3
|
E:GLU190
|
3.6
|
13.5
|
1.0
|
|
OD1
|
E:ASP185
|
3.6
|
10.8
|
1.0
|
|
OE1
|
E:GLU177
|
3.7
|
10.6
|
1.0
|
|
HB2
|
E:ASN183
|
3.7
|
24.1
|
1.0
|
|
HG2
|
E:GLU190
|
3.8
|
13.5
|
1.0
|
|
HB3
|
E:ASN183
|
3.8
|
24.1
|
1.0
|
|
CG
|
E:GLU190
|
3.8
|
11.3
|
1.0
|
|
CA
|
E:CA403
|
3.8
|
9.7
|
1.0
|
|
H
|
E:ASP185
|
4.0
|
13.5
|
1.0
|
|
CB
|
E:ASN183
|
4.1
|
20.1
|
1.0
|
|
CA
|
E:PRO184
|
4.2
|
12.8
|
1.0
|
|
N
|
E:ASP185
|
4.2
|
11.3
|
1.0
|
|
O
|
E:HOH538
|
4.2
|
31.3
|
1.0
|
|
OD1
|
E:ASP191
|
4.2
|
15.0
|
1.0
|
|
OE1
|
E:GLU190
|
4.3
|
10.6
|
1.0
|
|
CG
|
E:GLU177
|
4.3
|
10.2
|
1.0
|
|
OD2
|
E:ASP191
|
4.3
|
14.8
|
1.0
|
|
HG2
|
E:GLU177
|
4.3
|
12.2
|
1.0
|
|
C
|
E:PRO184
|
4.3
|
13.3
|
1.0
|
|
N
|
E:PRO184
|
4.3
|
13.2
|
1.0
|
|
HB3
|
E:ASP185
|
4.3
|
13.8
|
1.0
|
|
CB
|
E:ASP185
|
4.3
|
11.5
|
1.0
|
|
HG3
|
E:GLU177
|
4.4
|
12.2
|
1.0
|
|
O
|
E:LYS182
|
4.4
|
17.6
|
1.0
|
|
CA
|
E:ASN183
|
4.5
|
17.5
|
1.0
|
|
O
|
E:HOH556
|
4.5
|
33.9
|
1.0
|
|
CG
|
E:ASP191
|
4.6
|
13.7
|
1.0
|
|
O
|
E:HOH829
|
4.6
|
35.0
|
1.0
|
|
CA
|
E:ASP185
|
4.9
|
11.2
|
1.0
|
|
O
|
E:PRO184
|
5.0
|
14.6
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5n2t
Go back to
Calcium Binding Sites List in 5n2t
Calcium binding site 4 out
of 4 in the Thermolysin in Complex with Inhibitor JC287
 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 Inhibitor JC287 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca405
b:14.7
occ:1.00
|
O
|
E:ILE197
|
2.3
|
20.8
|
1.0
|
|
OG1
|
E:THR194
|
2.3
|
14.9
|
1.0
|
|
O
|
E:TYR193
|
2.4
|
14.5
|
1.0
|
|
O
|
E:THR194
|
2.4
|
16.0
|
1.0
|
|
OD1
|
E:ASP200
|
2.4
|
16.0
|
1.0
|
|
O
|
E:HOH574
|
2.4
|
16.3
|
1.0
|
|
O
|
E:HOH739
|
2.4
|
20.4
|
1.0
|
|
C
|
E:THR194
|
3.2
|
15.8
|
1.0
|
|
C
|
E:TYR193
|
3.3
|
14.1
|
1.0
|
|
CB
|
E:THR194
|
3.4
|
15.3
|
1.0
|
|
CG
|
E:ASP200
|
3.4
|
16.5
|
1.0
|
|
C
|
E:ILE197
|
3.5
|
21.0
|
1.0
|
|
HB
|
E:ILE197
|
3.5
|
28.8
|
1.0
|
|
H
|
E:ILE197
|
3.6
|
26.8
|
1.0
|
|
CA
|
E:THR194
|
3.6
|
15.3
|
1.0
|
|
HB
|
E:THR194
|
3.7
|
18.4
|
1.0
|
|
OD2
|
E:ASP200
|
3.8
|
17.6
|
1.0
|
|
N
|
E:THR194
|
3.9
|
14.3
|
1.0
|
|
H
|
E:ASP200
|
3.9
|
20.9
|
1.0
|
|
HD2
|
E:TYR193
|
4.0
|
18.1
|
1.0
|
|
HB3
|
E:TYR193
|
4.0
|
16.6
|
1.0
|
|
HA
|
E:SER198
|
4.1
|
28.2
|
1.0
|
|
CA
|
E:ILE197
|
4.2
|
21.9
|
1.0
|
|
N
|
E:PRO195
|
4.3
|
17.1
|
1.0
|
|
HA
|
E:PRO195
|
4.3
|
23.1
|
1.0
|
|
N
|
E:ILE197
|
4.3
|
22.3
|
1.0
|
|
CB
|
E:ILE197
|
4.3
|
24.0
|
1.0
|
|
HG22
|
E:ILE197
|
4.4
|
28.8
|
1.0
|
|
O
|
E:HOH613
|
4.5
|
38.7
|
1.0
|
|
O
|
E:ASP200
|
4.5
|
15.5
|
1.0
|
|
N
|
E:SER198
|
4.5
|
22.1
|
1.0
|
|
CA
|
E:TYR193
|
4.5
|
13.4
|
1.0
|
|
HA
|
E:THR194
|
4.6
|
18.4
|
1.0
|
|
CD2
|
E:TYR193
|
4.6
|
15.1
|
1.0
|
|
CB
|
E:TYR193
|
4.6
|
13.8
|
1.0
|
|
CA
|
E:SER198
|
4.7
|
23.5
|
1.0
|
|
O
|
E:GLU190
|
4.7
|
12.8
|
1.0
|
|
O
|
E:HOH769
|
4.7
|
28.5
|
1.0
|
|
N
|
E:ASP200
|
4.7
|
17.4
|
1.0
|
|
O
|
E:HOH705
|
4.7
|
40.4
|
1.0
|
|
CA
|
E:PRO195
|
4.7
|
19.3
|
1.0
|
|
CG2
|
E:THR194
|
4.7
|
16.2
|
1.0
|
|
H
|
E:THR194
|
4.7
|
17.1
|
1.0
|
|
H
|
E:GLY199
|
4.7
|
24.4
|
1.0
|
|
CB
|
E:ASP200
|
4.7
|
16.9
|
1.0
|
|
HG23
|
E:THR194
|
4.8
|
19.4
|
1.0
|
|
C
|
E:ASP200
|
4.8
|
15.9
|
1.0
|
|
H
|
E:TYR193
|
4.9
|
15.4
|
1.0
|
|
CG2
|
E:ILE197
|
4.9
|
24.0
|
1.0
|
|
C
|
E:PRO195
|
4.9
|
21.5
|
1.0
|
|
C
|
E:SER198
|
5.0
|
22.9
|
1.0
|
|
HG21
|
E:THR194
|
5.0
|
19.4
|
1.0
|
|
CA
|
E:ASP200
|
5.0
|
16.2
|
1.0
|
|
N
|
E:GLY199
|
5.0
|
20.4
|
1.0
|
|
CG
|
E:TYR193
|
5.0
|
14.6
|
1.0
|
|
Reference:
J.Cramer,
S.G.Krimmer,
A.Heine,
G.Klebe.
Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in A Series of Thermolysin Inhibitors. J. Med. Chem. V. 60 5791 2017.
ISSN: ISSN 1520-4804
PubMed: 28590130
DOI: 10.1021/ACS.JMEDCHEM.7B00490
Page generated: Mon Jul 15 08:43:14 2024
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