Calcium in PDB 5dpe: Thermolysin in Complex with Inhibitor.
Enzymatic activity of Thermolysin in Complex with Inhibitor.
All present enzymatic activity of Thermolysin in Complex with Inhibitor.:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with Inhibitor., PDB code: 5dpe
was solved by
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)
|
34.17 /
1.34
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.690,
92.690,
130.261,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
12.7 /
15.6
|
Other elements in 5dpe:
The structure of Thermolysin in Complex with Inhibitor. also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin in Complex with Inhibitor.
(pdb code 5dpe). 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., PDB code: 5dpe:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5dpe
Go back to
Calcium Binding Sites List in 5dpe
Calcium binding site 1 out
of 4 in the Thermolysin in Complex with Inhibitor.
 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. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:10.4
occ:1.00
|
O
|
E:GLU187
|
2.4
|
10.3
|
1.0
|
|
OD2
|
E:ASP138
|
2.4
|
11.0
|
1.0
|
|
O
|
E:HOH602
|
2.4
|
10.7
|
1.0
|
|
OE1
|
E:GLU177
|
2.5
|
10.6
|
1.0
|
|
OD1
|
E:ASP185
|
2.5
|
11.0
|
1.0
|
|
OE1
|
E:GLU190
|
2.5
|
11.1
|
1.0
|
|
OE2
|
E:GLU190
|
2.5
|
11.3
|
1.0
|
|
OE2
|
E:GLU177
|
2.7
|
11.5
|
1.0
|
|
CD
|
E:GLU190
|
2.8
|
10.5
|
1.0
|
|
CD
|
E:GLU177
|
2.9
|
10.3
|
1.0
|
|
CG
|
E:ASP138
|
3.4
|
11.6
|
1.0
|
|
C
|
E:GLU187
|
3.4
|
11.0
|
1.0
|
|
CG
|
E:ASP185
|
3.5
|
11.6
|
1.0
|
|
HB3
|
E:ASP138
|
3.6
|
12.0
|
1.0
|
|
HA
|
E:ILE188
|
3.6
|
12.5
|
1.0
|
|
H
|
E:GLY189
|
3.8
|
13.4
|
1.0
|
|
CA
|
E:CA405
|
3.8
|
12.8
|
1.0
|
|
OD2
|
E:ASP185
|
3.8
|
12.8
|
1.0
|
|
H
|
E:GLU187
|
3.8
|
13.9
|
1.0
|
|
HB2
|
E:GLU187
|
4.0
|
16.9
|
1.0
|
|
CB
|
E:ASP138
|
4.0
|
10.0
|
1.0
|
|
O
|
E:ASP185
|
4.1
|
11.5
|
1.0
|
|
H
|
E:ASP185
|
4.2
|
13.8
|
1.0
|
|
H
|
E:GLU190
|
4.2
|
12.8
|
1.0
|
|
N
|
E:GLU187
|
4.3
|
11.6
|
1.0
|
|
N
|
E:ILE188
|
4.3
|
10.1
|
1.0
|
|
HB2
|
E:ASP138
|
4.3
|
12.0
|
1.0
|
|
OD1
|
E:ASP138
|
4.3
|
12.2
|
1.0
|
|
CA
|
E:ILE188
|
4.3
|
10.4
|
1.0
|
|
CA
|
E:GLU187
|
4.3
|
11.8
|
1.0
|
|
CG
|
E:GLU190
|
4.3
|
12.2
|
1.0
|
|
HD13
|
E:ILE188
|
4.4
|
15.9
|
1.0
|
|
O
|
E:HOH580
|
4.4
|
16.3
|
1.0
|
|
CG
|
E:GLU177
|
4.4
|
10.3
|
1.0
|
|
N
|
E:GLY189
|
4.4
|
11.2
|
1.0
|
|
C
|
E:ASP185
|
4.6
|
10.6
|
1.0
|
|
HG3
|
E:GLU190
|
4.6
|
14.6
|
1.0
|
|
CB
|
E:GLU187
|
4.6
|
14.1
|
1.0
|
|
HB2
|
E:GLU177
|
4.7
|
11.8
|
1.0
|
|
HB3
|
E:GLU177
|
4.7
|
11.8
|
1.0
|
|
C
|
E:ILE188
|
4.8
|
10.7
|
1.0
|
|
CB
|
E:ASP185
|
4.8
|
11.5
|
1.0
|
|
N
|
E:ASP185
|
4.8
|
11.5
|
1.0
|
|
HG2
|
E:GLU190
|
4.8
|
14.6
|
1.0
|
|
HG2
|
E:GLU177
|
4.8
|
12.4
|
1.0
|
|
HA
|
E:THR174
|
4.9
|
11.1
|
1.0
|
|
CB
|
E:GLU177
|
4.9
|
9.8
|
1.0
|
|
HG3
|
E:GLU177
|
4.9
|
12.4
|
1.0
|
|
O
|
E:HOH560
|
4.9
|
15.2
|
1.0
|
|
HB3
|
E:GLU190
|
5.0
|
15.0
|
1.0
|
|
N
|
E:GLU190
|
5.0
|
10.7
|
1.0
|
|
CA
|
E:ASP185
|
5.0
|
11.1
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5dpe
Go back to
Calcium Binding Sites List in 5dpe
Calcium binding site 2 out
of 4 in the Thermolysin in Complex with Inhibitor.
 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. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca404
b:10.9
occ:1.00
|
O
|
E:GLN61
|
2.3
|
10.7
|
1.0
|
|
O
|
E:HOH780
|
2.3
|
13.3
|
1.0
|
|
OD1
|
E:ASP57
|
2.4
|
11.2
|
1.0
|
|
OD1
|
E:ASP59
|
2.4
|
11.1
|
1.0
|
|
O
|
E:HOH556
|
2.4
|
13.8
|
1.0
|
|
O
|
E:HOH605
|
2.4
|
12.6
|
1.0
|
|
OD2
|
E:ASP57
|
2.6
|
10.6
|
1.0
|
|
CG
|
E:ASP57
|
2.8
|
10.5
|
1.0
|
|
H
|
E:GLN61
|
3.3
|
12.5
|
0.6
|
|
H
|
E:GLN61
|
3.3
|
12.5
|
0.4
|
|
CG
|
E:ASP59
|
3.4
|
11.5
|
1.0
|
|
C
|
E:GLN61
|
3.4
|
10.0
|
1.0
|
|
HB2
|
E:GLN61
|
3.5
|
15.3
|
0.4
|
|
H
|
E:ASP59
|
3.5
|
12.8
|
1.0
|
|
HB2
|
E:GLN61
|
3.6
|
15.0
|
0.6
|
|
OD2
|
E:ASP59
|
3.8
|
13.8
|
1.0
|
|
N
|
E:GLN61
|
3.9
|
10.4
|
1.0
|
|
O
|
E:HOH699
|
4.0
|
16.9
|
1.0
|
|
HA
|
E:PHE62
|
4.1
|
11.6
|
1.0
|
|
CA
|
E:GLN61
|
4.1
|
10.9
|
0.4
|
|
CA
|
E:GLN61
|
4.1
|
10.8
|
0.6
|
|
CB
|
E:GLN61
|
4.3
|
12.8
|
0.4
|
|
H
|
E:ALA58
|
4.3
|
12.3
|
1.0
|
|
CB
|
E:GLN61
|
4.3
|
12.5
|
0.6
|
|
CB
|
E:ASP57
|
4.3
|
10.6
|
1.0
|
|
N
|
E:ASP59
|
4.3
|
10.7
|
1.0
|
|
H
|
E:ASN60
|
4.3
|
11.9
|
1.0
|
|
O
|
E:HOH728
|
4.4
|
14.3
|
1.0
|
|
N
|
E:PHE62
|
4.5
|
9.4
|
1.0
|
|
O
|
E:HOH853
|
4.5
|
21.6
|
1.0
|
|
CB
|
E:ASP59
|
4.6
|
10.6
|
1.0
|
|
O
|
E:HOH524
|
4.6
|
10.8
|
1.0
|
|
N
|
E:ASN60
|
4.6
|
9.9
|
1.0
|
|
OD2
|
E:ASP67
|
4.6
|
10.5
|
1.0
|
|
O
|
E:HOH839
|
4.7
|
30.3
|
1.0
|
|
HB2
|
E:ASP57
|
4.7
|
12.7
|
1.0
|
|
N
|
E:ALA58
|
4.7
|
10.3
|
1.0
|
|
HB3
|
E:ASP57
|
4.8
|
12.7
|
1.0
|
|
O
|
E:HOH872
|
4.8
|
31.0
|
1.0
|
|
CA
|
E:PHE62
|
4.8
|
9.7
|
1.0
|
|
CA
|
E:ASP59
|
4.8
|
10.2
|
1.0
|
|
HB3
|
E:GLN61
|
4.8
|
15.0
|
0.6
|
|
H
|
E:PHE63
|
4.9
|
12.8
|
1.0
|
|
HB3
|
E:GLN61
|
4.9
|
15.3
|
0.4
|
|
HA
|
E:ASP57
|
4.9
|
12.3
|
1.0
|
|
C
|
E:ASP59
|
4.9
|
9.7
|
1.0
|
|
HB3
|
E:ASP59
|
5.0
|
12.7
|
1.0
|
|
HB3
|
E:ALA58
|
5.0
|
14.0
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5dpe
Go back to
Calcium Binding Sites List in 5dpe
Calcium binding site 3 out
of 4 in the Thermolysin in Complex with Inhibitor.
 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. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca405
b:12.8
occ:1.00
|
O
|
E:ASN183
|
2.3
|
14.5
|
1.0
|
|
OE2
|
E:GLU190
|
2.3
|
11.3
|
1.0
|
|
OD2
|
E:ASP185
|
2.3
|
12.8
|
1.0
|
|
O
|
E:HOH560
|
2.3
|
15.2
|
1.0
|
|
O
|
E:HOH631
|
2.3
|
15.0
|
1.0
|
|
OE2
|
E:GLU177
|
2.4
|
11.5
|
1.0
|
|
CG
|
E:ASP185
|
3.2
|
11.6
|
1.0
|
|
CD
|
E:GLU177
|
3.2
|
10.3
|
1.0
|
|
CD
|
E:GLU190
|
3.3
|
10.5
|
1.0
|
|
C
|
E:ASN183
|
3.5
|
14.7
|
1.0
|
|
HA
|
E:PRO184
|
3.6
|
15.1
|
1.0
|
|
HG3
|
E:GLU190
|
3.6
|
14.6
|
1.0
|
|
OD1
|
E:ASP185
|
3.6
|
11.0
|
1.0
|
|
HB2
|
E:ASN183
|
3.7
|
22.9
|
1.0
|
|
OE1
|
E:GLU177
|
3.8
|
10.6
|
1.0
|
|
HG2
|
E:GLU190
|
3.8
|
14.6
|
1.0
|
|
HB3
|
E:ASN183
|
3.8
|
22.9
|
1.0
|
|
CA
|
E:CA403
|
3.8
|
10.4
|
1.0
|
|
CG
|
E:GLU190
|
3.8
|
12.2
|
1.0
|
|
H
|
E:ASP185
|
3.9
|
13.8
|
1.0
|
|
N
|
E:ASP185
|
4.1
|
11.5
|
1.0
|
|
CA
|
E:PRO184
|
4.1
|
12.6
|
1.0
|
|
CB
|
E:ASN183
|
4.1
|
19.1
|
1.0
|
|
HG2
|
E:GLU177
|
4.2
|
12.4
|
1.0
|
|
O
|
E:HOH740
|
4.2
|
41.0
|
1.0
|
|
C
|
E:PRO184
|
4.2
|
12.6
|
1.0
|
|
CG
|
E:GLU177
|
4.2
|
10.3
|
1.0
|
|
OD2
|
E:ASP191
|
4.3
|
16.6
|
1.0
|
|
OD1
|
E:ASP191
|
4.3
|
16.2
|
1.0
|
|
N
|
E:PRO184
|
4.3
|
12.8
|
1.0
|
|
OE1
|
E:GLU190
|
4.3
|
11.1
|
1.0
|
|
HG3
|
E:GLU177
|
4.3
|
12.4
|
1.0
|
|
HB3
|
E:ASP185
|
4.4
|
13.8
|
1.0
|
|
CB
|
E:ASP185
|
4.4
|
11.5
|
1.0
|
|
O
|
E:LYS182
|
4.4
|
17.3
|
1.0
|
|
CA
|
E:ASN183
|
4.5
|
17.1
|
1.0
|
|
CG
|
E:ASP191
|
4.6
|
14.7
|
1.0
|
|
O
|
E:HOH855
|
4.6
|
31.8
|
1.0
|
|
CA
|
E:ASP185
|
4.9
|
11.1
|
1.0
|
|
O
|
E:PRO184
|
4.9
|
14.2
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5dpe
Go back to
Calcium Binding Sites List in 5dpe
Calcium binding site 4 out
of 4 in the Thermolysin in Complex with Inhibitor.
 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. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca406
b:13.1
occ:1.00
|
O
|
E:ILE197
|
2.3
|
17.3
|
1.0
|
|
O
|
E:TYR193
|
2.4
|
13.3
|
1.0
|
|
OG1
|
E:THR194
|
2.4
|
14.7
|
1.0
|
|
OD1
|
E:ASP200
|
2.4
|
13.9
|
1.0
|
|
O
|
E:HOH615
|
2.4
|
16.1
|
1.0
|
|
O
|
E:THR194
|
2.4
|
14.5
|
1.0
|
|
O
|
E:HOH751
|
2.4
|
18.9
|
1.0
|
|
C
|
E:THR194
|
3.2
|
14.4
|
1.0
|
|
C
|
E:TYR193
|
3.4
|
13.0
|
1.0
|
|
CB
|
E:THR194
|
3.4
|
14.4
|
1.0
|
|
CG
|
E:ASP200
|
3.4
|
14.3
|
1.0
|
|
HB
|
E:ILE197
|
3.5
|
23.8
|
1.0
|
|
C
|
E:ILE197
|
3.5
|
17.8
|
1.0
|
|
CA
|
E:THR194
|
3.6
|
14.0
|
1.0
|
|
H
|
E:ILE197
|
3.7
|
23.9
|
1.0
|
|
HB
|
E:THR194
|
3.7
|
17.3
|
1.0
|
|
OD2
|
E:ASP200
|
3.8
|
14.7
|
1.0
|
|
H
|
E:ASP200
|
3.9
|
17.2
|
1.0
|
|
N
|
E:THR194
|
3.9
|
13.2
|
1.0
|
|
HA
|
E:SER198
|
4.0
|
23.9
|
1.0
|
|
HB3
|
E:TYR193
|
4.1
|
16.1
|
1.0
|
|
HD2
|
E:TYR193
|
4.1
|
18.6
|
1.0
|
|
CA
|
E:ILE197
|
4.3
|
18.7
|
1.0
|
|
CB
|
E:ILE197
|
4.3
|
19.8
|
1.0
|
|
N
|
E:PRO195
|
4.3
|
15.7
|
1.0
|
|
N
|
E:ILE197
|
4.3
|
19.9
|
1.0
|
|
HA
|
E:PRO195
|
4.4
|
20.3
|
1.0
|
|
O
|
E:HOH764
|
4.4
|
45.4
|
1.0
|
|
HG22
|
E:ILE197
|
4.5
|
23.6
|
1.0
|
|
O
|
E:ASP200
|
4.5
|
13.1
|
1.0
|
|
N
|
E:SER198
|
4.5
|
18.8
|
1.0
|
|
CA
|
E:TYR193
|
4.6
|
13.0
|
1.0
|
|
HA
|
E:THR194
|
4.6
|
16.8
|
1.0
|
|
O
|
E:HOH707
|
4.6
|
32.3
|
1.0
|
|
O
|
E:HOH784
|
4.6
|
27.6
|
1.0
|
|
O
|
E:GLU190
|
4.6
|
12.7
|
1.0
|
|
CD2
|
E:TYR193
|
4.6
|
15.5
|
1.0
|
|
CA
|
E:SER198
|
4.7
|
19.9
|
1.0
|
|
N
|
E:ASP200
|
4.7
|
14.3
|
1.0
|
|
CB
|
E:TYR193
|
4.7
|
13.4
|
1.0
|
|
H
|
E:GLY199
|
4.7
|
20.3
|
1.0
|
|
CG2
|
E:THR194
|
4.7
|
14.4
|
1.0
|
|
CA
|
E:PRO195
|
4.7
|
16.9
|
1.0
|
|
CB
|
E:ASP200
|
4.7
|
14.1
|
1.0
|
|
H
|
E:THR194
|
4.8
|
15.8
|
1.0
|
|
HG23
|
E:THR194
|
4.8
|
17.2
|
1.0
|
|
C
|
E:ASP200
|
4.8
|
13.5
|
1.0
|
|
CG2
|
E:ILE197
|
4.9
|
19.7
|
1.0
|
|
H
|
E:TYR193
|
4.9
|
14.1
|
1.0
|
|
HG21
|
E:THR194
|
5.0
|
17.2
|
1.0
|
|
C
|
E:SER198
|
5.0
|
18.7
|
1.0
|
|
CG
|
E:TYR193
|
5.0
|
14.5
|
1.0
|
|
CA
|
E:ASP200
|
5.0
|
14.1
|
1.0
|
|
N
|
E:GLY199
|
5.0
|
16.9
|
1.0
|
|
Reference:
S.G.Krimmer,
G.Klebe.
Thermodynamics of Protein-Ligand Interactions As A Reference For Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data. J. Comput. Aided Mol. Des. V. 29 867 2015.
ISSN: ISSN 1573-4951
PubMed: 26376645
DOI: 10.1007/S10822-015-9867-Y
Page generated: Sun Jul 14 18:06:23 2024
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