Calcium in PDB 5lvd: Thermolysin in Complex with Inhibitor (JC67)
Enzymatic activity of Thermolysin in Complex with Inhibitor (JC67)
All present enzymatic activity of Thermolysin in Complex with Inhibitor (JC67):
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with Inhibitor (JC67), PDB code: 5lvd
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)
|
38.24 /
1.25
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.846,
92.846,
130.426,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
10.5 /
12.5
|
Other elements in 5lvd:
The structure of Thermolysin in Complex with Inhibitor (JC67) also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin in Complex with Inhibitor (JC67)
(pdb code 5lvd). 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 (JC67), PDB code: 5lvd:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5lvd
Go back to
Calcium Binding Sites List in 5lvd
Calcium binding site 1 out
of 4 in the Thermolysin in Complex with Inhibitor (JC67)
 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 (JC67) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:8.7
occ:1.00
|
O
|
E:GLU187
|
2.3
|
9.1
|
1.0
|
|
OD2
|
E:ASP138
|
2.4
|
8.5
|
1.0
|
|
O
|
E:HOH587
|
2.4
|
9.2
|
1.0
|
|
OE1
|
E:GLU177
|
2.5
|
9.1
|
1.0
|
|
OD1
|
E:ASP185
|
2.5
|
10.1
|
1.0
|
|
OE1
|
E:GLU190
|
2.5
|
9.3
|
1.0
|
|
OE2
|
E:GLU190
|
2.5
|
10.1
|
1.0
|
|
OE2
|
E:GLU177
|
2.7
|
10.5
|
1.0
|
|
CD
|
E:GLU190
|
2.9
|
9.4
|
1.0
|
|
CD
|
E:GLU177
|
2.9
|
8.8
|
1.0
|
|
CG
|
E:ASP138
|
3.4
|
8.3
|
1.0
|
|
C
|
E:GLU187
|
3.4
|
9.7
|
1.0
|
|
CG
|
E:ASP185
|
3.5
|
10.8
|
1.0
|
|
HB3
|
E:ASP138
|
3.6
|
8.8
|
1.0
|
|
HA
|
E:ILE188
|
3.6
|
10.4
|
1.0
|
|
H
|
E:GLU187
|
3.7
|
12.8
|
1.0
|
|
H
|
E:GLY189
|
3.8
|
10.8
|
1.0
|
|
CA
|
E:CA405
|
3.8
|
13.3
|
1.0
|
|
OD2
|
E:ASP185
|
3.8
|
13.0
|
1.0
|
|
HB2
|
E:GLU187
|
3.8
|
15.9
|
1.0
|
|
CB
|
E:ASP138
|
4.0
|
7.3
|
1.0
|
|
H
|
E:ASP185
|
4.1
|
12.9
|
1.0
|
|
O
|
E:ASP185
|
4.1
|
10.1
|
1.0
|
|
H
|
E:GLU190
|
4.2
|
11.3
|
1.0
|
|
N
|
E:GLU187
|
4.2
|
10.7
|
1.0
|
|
N
|
E:ILE188
|
4.2
|
8.9
|
1.0
|
|
OD1
|
E:ASP138
|
4.3
|
9.3
|
1.0
|
|
HB2
|
E:ASP138
|
4.3
|
8.8
|
1.0
|
|
CA
|
E:GLU187
|
4.3
|
10.9
|
1.0
|
|
CA
|
E:ILE188
|
4.3
|
8.7
|
1.0
|
|
CG
|
E:GLU190
|
4.4
|
9.8
|
1.0
|
|
O
|
E:HOH603
|
4.4
|
13.9
|
1.0
|
|
HD13
|
E:ILE188
|
4.4
|
14.0
|
1.0
|
|
CG
|
E:GLU177
|
4.4
|
8.8
|
1.0
|
|
N
|
E:GLY189
|
4.4
|
9.0
|
1.0
|
|
CB
|
E:GLU187
|
4.5
|
13.2
|
1.0
|
|
C
|
E:ASP185
|
4.6
|
10.2
|
1.0
|
|
HG3
|
E:GLU190
|
4.6
|
11.8
|
1.0
|
|
HB2
|
E:GLU177
|
4.7
|
10.0
|
1.0
|
|
N
|
E:ASP185
|
4.7
|
10.8
|
1.0
|
|
CB
|
E:ASP185
|
4.8
|
10.8
|
1.0
|
|
HB3
|
E:GLU177
|
4.8
|
10.0
|
1.0
|
|
O
|
E:HOH540
|
4.8
|
17.0
|
1.0
|
|
C
|
E:ILE188
|
4.8
|
9.0
|
1.0
|
|
HG2
|
E:GLU177
|
4.8
|
10.5
|
1.0
|
|
HG2
|
E:GLU190
|
4.8
|
11.8
|
1.0
|
|
HA
|
E:THR174
|
4.9
|
9.0
|
1.0
|
|
HG3
|
E:GLU177
|
4.9
|
10.5
|
1.0
|
|
CB
|
E:GLU177
|
4.9
|
8.3
|
1.0
|
|
CA
|
E:ASP185
|
5.0
|
10.7
|
1.0
|
|
HB3
|
E:GLU190
|
5.0
|
12.3
|
1.0
|
|
N
|
E:GLU190
|
5.0
|
9.4
|
1.0
|
|
HB3
|
E:GLU187
|
5.0
|
15.9
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5lvd
Go back to
Calcium Binding Sites List in 5lvd
Calcium binding site 2 out
of 4 in the Thermolysin in Complex with Inhibitor (JC67)
 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 (JC67) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:8.6
occ:1.00
|
O
|
E:GLN61
|
2.3
|
8.6
|
1.0
|
|
O
|
E:HOH775
|
2.3
|
11.0
|
1.0
|
|
OD1
|
E:ASP57
|
2.4
|
9.0
|
1.0
|
|
OD1
|
E:ASP59
|
2.4
|
9.6
|
1.0
|
|
O
|
E:HOH580
|
2.4
|
10.8
|
1.0
|
|
O
|
E:HOH582
|
2.4
|
9.9
|
1.0
|
|
OD2
|
E:ASP57
|
2.6
|
8.6
|
1.0
|
|
CG
|
E:ASP57
|
2.8
|
8.3
|
1.0
|
|
H
|
E:GLN61
|
3.3
|
9.8
|
1.0
|
|
CG
|
E:ASP59
|
3.4
|
9.9
|
1.0
|
|
C
|
E:GLN61
|
3.5
|
7.9
|
1.0
|
|
H
|
E:ASP59
|
3.5
|
10.3
|
1.0
|
|
HB2
|
E:GLN61
|
3.6
|
14.3
|
1.0
|
|
OD2
|
E:ASP59
|
3.8
|
12.1
|
1.0
|
|
N
|
E:GLN61
|
4.0
|
8.2
|
1.0
|
|
O
|
E:HOH699
|
4.0
|
15.4
|
1.0
|
|
HA
|
E:PHE62
|
4.0
|
9.4
|
1.0
|
|
CA
|
E:GLN61
|
4.2
|
8.7
|
1.0
|
|
H
|
E:ALA58
|
4.3
|
9.9
|
1.0
|
|
N
|
E:ASP59
|
4.3
|
8.6
|
1.0
|
|
CB
|
E:ASP57
|
4.3
|
8.4
|
1.0
|
|
CB
|
E:GLN61
|
4.3
|
11.9
|
1.0
|
|
H
|
E:ASN60
|
4.4
|
9.7
|
1.0
|
|
O
|
E:HOH743
|
4.5
|
11.2
|
1.0
|
|
N
|
E:PHE62
|
4.5
|
7.6
|
1.0
|
|
O
|
E:HOH843
|
4.6
|
14.0
|
1.0
|
|
CB
|
E:ASP59
|
4.6
|
9.6
|
1.0
|
|
OD2
|
E:ASP67
|
4.6
|
8.6
|
1.0
|
|
O
|
E:HOH521
|
4.6
|
8.2
|
1.0
|
|
O
|
E:HOH830
|
4.6
|
24.3
|
1.0
|
|
N
|
E:ASN60
|
4.7
|
8.1
|
1.0
|
|
O
|
E:HOH868
|
4.7
|
28.3
|
1.0
|
|
HB2
|
E:ASP57
|
4.7
|
10.1
|
1.0
|
|
N
|
E:ALA58
|
4.7
|
8.3
|
1.0
|
|
CA
|
E:PHE62
|
4.8
|
7.8
|
1.0
|
|
CA
|
E:ASP59
|
4.8
|
9.2
|
1.0
|
|
HB3
|
E:ASP57
|
4.8
|
10.1
|
1.0
|
|
H
|
E:PHE63
|
4.8
|
10.4
|
1.0
|
|
HA
|
E:ASP57
|
4.9
|
9.9
|
1.0
|
|
C
|
E:ASP59
|
4.9
|
8.7
|
1.0
|
|
HB3
|
E:ASP59
|
5.0
|
11.6
|
1.0
|
|
HB3
|
E:GLN61
|
5.0
|
14.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5lvd
Go back to
Calcium Binding Sites List in 5lvd
Calcium binding site 3 out
of 4 in the Thermolysin in Complex with Inhibitor (JC67)
 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 (JC67) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca404
b:12.6
occ:1.00
|
O
|
E:ILE197
|
2.3
|
19.0
|
1.0
|
|
O
|
E:TYR193
|
2.4
|
11.6
|
1.0
|
|
OG1
|
E:THR194
|
2.4
|
13.1
|
1.0
|
|
OD2
|
E:ASP200
|
2.4
|
14.2
|
1.0
|
|
O
|
E:HOH760
|
2.4
|
19.3
|
1.0
|
|
O
|
E:THR194
|
2.4
|
14.0
|
1.0
|
|
O
|
E:HOH581
|
2.4
|
14.8
|
1.0
|
|
C
|
E:THR194
|
3.2
|
13.8
|
1.0
|
|
C
|
E:TYR193
|
3.4
|
11.4
|
1.0
|
|
CG
|
E:ASP200
|
3.4
|
14.4
|
1.0
|
|
CB
|
E:THR194
|
3.4
|
13.6
|
1.0
|
|
HB
|
E:ILE197
|
3.5
|
26.1
|
1.0
|
|
C
|
E:ILE197
|
3.5
|
20.2
|
1.0
|
|
H
|
E:ILE197
|
3.6
|
23.9
|
1.0
|
|
CA
|
E:THR194
|
3.6
|
12.7
|
1.0
|
|
HB
|
E:THR194
|
3.7
|
16.4
|
1.0
|
|
OD1
|
E:ASP200
|
3.8
|
15.7
|
1.0
|
|
H
|
E:ASP200
|
3.9
|
20.9
|
1.0
|
|
N
|
E:THR194
|
3.9
|
11.8
|
1.0
|
|
HA
|
E:SER198
|
4.0
|
26.9
|
0.5
|
|
HB3
|
E:TYR193
|
4.1
|
14.4
|
1.0
|
|
HD2
|
E:TYR193
|
4.1
|
17.7
|
1.0
|
|
HA
|
E:SER198
|
4.2
|
26.7
|
0.6
|
|
CA
|
E:ILE197
|
4.2
|
20.1
|
1.0
|
|
CB
|
E:ILE197
|
4.2
|
21.8
|
1.0
|
|
N
|
E:PRO195
|
4.3
|
14.6
|
1.0
|
|
N
|
E:ILE197
|
4.3
|
19.9
|
1.0
|
|
HA
|
E:PRO195
|
4.3
|
20.0
|
1.0
|
|
HG22
|
E:ILE197
|
4.4
|
26.0
|
1.0
|
|
O
|
E:ASP200
|
4.5
|
14.9
|
1.0
|
|
O
|
E:HOH668
|
4.5
|
40.6
|
1.0
|
|
N
|
E:SER198
|
4.5
|
21.2
|
0.5
|
|
N
|
E:SER198
|
4.5
|
21.1
|
0.6
|
|
O
|
E:HOH667
|
4.5
|
41.9
|
1.0
|
|
CA
|
E:TYR193
|
4.5
|
11.0
|
1.0
|
|
O
|
E:HOH670
|
4.6
|
42.2
|
1.0
|
|
HA
|
E:THR194
|
4.6
|
15.2
|
1.0
|
|
O
|
E:GLU190
|
4.6
|
11.6
|
1.0
|
|
CD2
|
E:TYR193
|
4.6
|
14.8
|
1.0
|
|
CA
|
E:SER198
|
4.7
|
22.4
|
0.5
|
|
N
|
E:ASP200
|
4.7
|
17.4
|
1.0
|
|
CB
|
E:TYR193
|
4.7
|
12.0
|
1.0
|
|
O
|
E:HOH781
|
4.7
|
22.9
|
1.0
|
|
CA
|
E:PRO195
|
4.7
|
16.6
|
1.0
|
|
CA
|
E:SER198
|
4.7
|
22.2
|
0.6
|
|
CG2
|
E:THR194
|
4.7
|
14.0
|
1.0
|
|
H
|
E:THR194
|
4.7
|
14.2
|
1.0
|
|
CB
|
E:ASP200
|
4.8
|
15.7
|
1.0
|
|
H
|
E:GLY199
|
4.8
|
25.4
|
1.0
|
|
C
|
E:ASP200
|
4.8
|
14.8
|
1.0
|
|
CG2
|
E:ILE197
|
4.8
|
21.6
|
1.0
|
|
HG23
|
E:THR194
|
4.8
|
16.9
|
1.0
|
|
H
|
E:TYR193
|
4.9
|
12.0
|
1.0
|
|
C
|
E:SER198
|
5.0
|
22.3
|
0.6
|
|
C
|
E:PRO195
|
5.0
|
18.9
|
1.0
|
|
HG21
|
E:THR194
|
5.0
|
16.9
|
1.0
|
|
CA
|
E:ASP200
|
5.0
|
15.8
|
1.0
|
|
CG
|
E:TYR193
|
5.0
|
13.9
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5lvd
Go back to
Calcium Binding Sites List in 5lvd
Calcium binding site 4 out
of 4 in the Thermolysin in Complex with Inhibitor (JC67)
 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 (JC67) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca405
b:13.3
occ:1.00
|
OE2
|
E:GLU190
|
2.3
|
10.1
|
1.0
|
|
O
|
E:ASN183
|
2.3
|
15.0
|
1.0
|
|
O
|
E:HOH563
|
2.3
|
15.7
|
1.0
|
|
O
|
E:HOH540
|
2.3
|
17.0
|
1.0
|
|
OD2
|
E:ASP185
|
2.3
|
13.0
|
1.0
|
|
OE2
|
E:GLU177
|
2.5
|
10.5
|
1.0
|
|
CG
|
E:ASP185
|
3.2
|
10.8
|
1.0
|
|
CD
|
E:GLU177
|
3.3
|
8.8
|
1.0
|
|
CD
|
E:GLU190
|
3.3
|
9.4
|
1.0
|
|
C
|
E:ASN183
|
3.5
|
15.5
|
1.0
|
|
HA
|
E:PRO184
|
3.5
|
14.2
|
1.0
|
|
HG3
|
E:GLU190
|
3.6
|
11.8
|
1.0
|
|
OD1
|
E:ASP185
|
3.6
|
10.1
|
1.0
|
|
OE1
|
E:GLU177
|
3.7
|
9.1
|
1.0
|
|
CA
|
E:CA402
|
3.8
|
8.7
|
1.0
|
|
HB2
|
E:ASN183
|
3.8
|
26.6
|
1.0
|
|
HG2
|
E:GLU190
|
3.8
|
11.8
|
1.0
|
|
CG
|
E:GLU190
|
3.8
|
9.8
|
1.0
|
|
HB3
|
E:ASN183
|
3.9
|
26.6
|
1.0
|
|
H
|
E:ASP185
|
4.0
|
12.9
|
1.0
|
|
CA
|
E:PRO184
|
4.1
|
11.9
|
1.0
|
|
N
|
E:ASP185
|
4.2
|
10.8
|
1.0
|
|
CB
|
E:ASN183
|
4.2
|
22.1
|
1.0
|
|
OD1
|
E:ASP191
|
4.3
|
13.7
|
1.0
|
|
OD2
|
E:ASP191
|
4.3
|
13.6
|
1.0
|
|
OE1
|
E:GLU190
|
4.3
|
9.3
|
1.0
|
|
HG2
|
E:GLU177
|
4.3
|
10.5
|
1.0
|
|
CG
|
E:GLU177
|
4.3
|
8.8
|
1.0
|
|
C
|
E:PRO184
|
4.3
|
12.0
|
1.0
|
|
N
|
E:PRO184
|
4.3
|
13.1
|
1.0
|
|
HB3
|
E:ASP185
|
4.3
|
13.0
|
1.0
|
|
HG3
|
E:GLU177
|
4.4
|
10.5
|
1.0
|
|
CB
|
E:ASP185
|
4.4
|
10.8
|
1.0
|
|
O
|
E:LYS182
|
4.5
|
19.2
|
1.0
|
|
CA
|
E:ASN183
|
4.5
|
18.8
|
1.0
|
|
O
|
E:HOH583
|
4.6
|
38.7
|
1.0
|
|
CG
|
E:ASP191
|
4.6
|
12.5
|
1.0
|
|
CA
|
E:ASP185
|
4.9
|
10.7
|
1.0
|
|
O
|
E:PRO184
|
5.0
|
13.8
|
1.0
|
|
Reference:
S.G.Krimmer,
J.Cramer,
J.Schiebel,
A.Heine,
G.Klebe.
How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin. J. Am. Chem. Soc. V. 139 10419 2017.
ISSN: ESSN 1520-5126
PubMed: 28696673
DOI: 10.1021/JACS.7B05028
Page generated: Mon Jul 15 07:49:09 2024
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