Calcium in PDB 5jt9: Thermolysin in Complex with JC106.
Enzymatic activity of Thermolysin in Complex with JC106.
All present enzymatic activity of Thermolysin in Complex with JC106.:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with JC106., PDB code: 5jt9
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)
|
34.20 /
1.26
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.547,
92.547,
131.226,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
10.3 /
12.1
|
Other elements in 5jt9:
The structure of Thermolysin in Complex with JC106. also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin in Complex with JC106.
(pdb code 5jt9). 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 JC106., PDB code: 5jt9:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5jt9
Go back to
Calcium Binding Sites List in 5jt9
Calcium binding site 1 out
of 4 in the Thermolysin in Complex with JC106.
 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 JC106. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:7.3
occ:1.00
|
O
|
E:GLU187
|
2.4
|
8.0
|
1.0
|
|
OD2
|
E:ASP138
|
2.4
|
7.5
|
1.0
|
|
O
|
E:HOH574
|
2.4
|
7.7
|
1.0
|
|
OD1
|
E:ASP185
|
2.5
|
8.0
|
1.0
|
|
OE1
|
E:GLU177
|
2.5
|
7.9
|
1.0
|
|
OE1
|
E:GLU190
|
2.5
|
8.2
|
1.0
|
|
OE2
|
E:GLU190
|
2.5
|
8.9
|
1.0
|
|
OE2
|
E:GLU177
|
2.7
|
8.5
|
1.0
|
|
CD
|
E:GLU190
|
2.8
|
7.9
|
1.0
|
|
CD
|
E:GLU177
|
2.9
|
7.3
|
1.0
|
|
CG
|
E:ASP138
|
3.4
|
7.4
|
1.0
|
|
C
|
E:GLU187
|
3.4
|
7.8
|
1.0
|
|
CG
|
E:ASP185
|
3.5
|
8.5
|
1.0
|
|
HB3
|
E:ASP138
|
3.6
|
7.5
|
1.0
|
|
HA
|
E:ILE188
|
3.7
|
8.4
|
1.0
|
|
H
|
E:GLU187
|
3.7
|
10.0
|
1.0
|
|
CA
|
E:CA404
|
3.8
|
10.6
|
1.0
|
|
OD2
|
E:ASP185
|
3.8
|
10.1
|
1.0
|
|
H
|
E:GLY189
|
3.8
|
8.8
|
1.0
|
|
HB2
|
E:GLU187
|
3.9
|
11.3
|
1.0
|
|
CB
|
E:ASP138
|
4.0
|
6.3
|
1.0
|
|
O
|
E:ASP185
|
4.1
|
8.1
|
1.0
|
|
H
|
E:ASP185
|
4.1
|
10.5
|
1.0
|
|
H
|
E:GLU190
|
4.2
|
9.5
|
1.0
|
|
N
|
E:GLU187
|
4.2
|
8.3
|
1.0
|
|
OD1
|
E:ASP138
|
4.2
|
8.7
|
1.0
|
|
N
|
E:ILE188
|
4.3
|
7.2
|
1.0
|
|
HB2
|
E:ASP138
|
4.3
|
7.5
|
1.0
|
|
CA
|
E:GLU187
|
4.3
|
8.4
|
1.0
|
|
O
|
E:HOH616
|
4.3
|
28.8
|
0.5
|
|
CA
|
E:ILE188
|
4.3
|
7.0
|
1.0
|
|
CG
|
E:GLU190
|
4.3
|
8.9
|
1.0
|
|
CG
|
E:GLU177
|
4.4
|
7.4
|
1.0
|
|
O
|
E:HOH562
|
4.4
|
12.0
|
1.0
|
|
HD13
|
E:ILE188
|
4.4
|
12.1
|
1.0
|
|
N
|
E:GLY189
|
4.4
|
7.3
|
1.0
|
|
CB
|
E:GLU187
|
4.6
|
9.4
|
1.0
|
|
C
|
E:ASP185
|
4.6
|
7.7
|
1.0
|
|
HG3
|
E:GLU190
|
4.6
|
10.7
|
1.0
|
|
HB2
|
E:GLU177
|
4.7
|
8.9
|
1.0
|
|
HB3
|
E:GLU177
|
4.7
|
8.9
|
1.0
|
|
N
|
E:ASP185
|
4.7
|
8.8
|
1.0
|
|
HG2
|
E:GLU177
|
4.8
|
8.9
|
1.0
|
|
CB
|
E:ASP185
|
4.8
|
8.8
|
1.0
|
|
C
|
E:ILE188
|
4.8
|
7.0
|
1.0
|
|
HG2
|
E:GLU190
|
4.8
|
10.7
|
1.0
|
|
O
|
E:HOH539
|
4.8
|
14.3
|
1.0
|
|
HA
|
E:THR174
|
4.9
|
7.5
|
1.0
|
|
CB
|
E:GLU177
|
4.9
|
7.4
|
1.0
|
|
HG3
|
E:GLU177
|
4.9
|
8.9
|
1.0
|
|
HB3
|
E:GLU190
|
4.9
|
10.5
|
1.0
|
|
CA
|
E:ASP185
|
5.0
|
8.5
|
1.0
|
|
N
|
E:GLU190
|
5.0
|
7.9
|
1.0
|
|
HB3
|
E:GLU187
|
5.0
|
11.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5jt9
Go back to
Calcium Binding Sites List in 5jt9
Calcium binding site 2 out
of 4 in the Thermolysin in Complex with JC106.
 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 JC106. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:7.8
occ:1.00
|
O
|
E:GLN61
|
2.3
|
8.2
|
1.0
|
|
O
|
E:HOH793
|
2.3
|
10.7
|
1.0
|
|
OD1
|
E:ASP59
|
2.4
|
8.7
|
1.0
|
|
OD1
|
E:ASP57
|
2.4
|
8.5
|
1.0
|
|
O
|
E:HOH557
|
2.4
|
10.1
|
1.0
|
|
O
|
E:HOH584
|
2.4
|
9.3
|
1.0
|
|
OD2
|
E:ASP57
|
2.6
|
8.3
|
1.0
|
|
CG
|
E:ASP57
|
2.8
|
8.0
|
1.0
|
|
H
|
E:GLN61
|
3.3
|
9.3
|
1.0
|
|
CG
|
E:ASP59
|
3.4
|
9.2
|
1.0
|
|
C
|
E:GLN61
|
3.5
|
7.5
|
1.0
|
|
H
|
E:ASP59
|
3.5
|
10.2
|
1.0
|
|
HB2
|
E:GLN61
|
3.6
|
12.7
|
1.0
|
|
OD2
|
E:ASP59
|
3.8
|
11.4
|
1.0
|
|
N
|
E:GLN61
|
4.0
|
7.7
|
1.0
|
|
O
|
E:HOH707
|
4.0
|
15.0
|
1.0
|
|
HA
|
E:PHE62
|
4.0
|
8.6
|
1.0
|
|
CA
|
E:GLN61
|
4.2
|
8.1
|
1.0
|
|
H
|
E:ALA58
|
4.3
|
8.9
|
1.0
|
|
N
|
E:ASP59
|
4.3
|
8.5
|
1.0
|
|
CB
|
E:GLN61
|
4.3
|
10.6
|
1.0
|
|
CB
|
E:ASP57
|
4.3
|
7.9
|
1.0
|
|
H
|
E:ASN60
|
4.4
|
9.1
|
1.0
|
|
O
|
E:HOH745
|
4.5
|
10.5
|
1.0
|
|
N
|
E:PHE62
|
4.5
|
6.9
|
1.0
|
|
O
|
E:HOH876
|
4.6
|
15.1
|
1.0
|
|
CB
|
E:ASP59
|
4.6
|
8.9
|
1.0
|
|
O
|
E:HOH523
|
4.6
|
7.6
|
1.0
|
|
N
|
E:ASN60
|
4.6
|
7.6
|
1.0
|
|
OD2
|
E:ASP67
|
4.6
|
7.7
|
1.0
|
|
O
|
E:HOH867
|
4.7
|
30.9
|
1.0
|
|
HB2
|
E:ASP57
|
4.7
|
9.5
|
1.0
|
|
O
|
E:HOH901
|
4.7
|
25.1
|
1.0
|
|
N
|
E:ALA58
|
4.7
|
7.5
|
1.0
|
|
CA
|
E:ASP59
|
4.8
|
8.5
|
1.0
|
|
CA
|
E:PHE62
|
4.8
|
7.1
|
1.0
|
|
HB3
|
E:ASP57
|
4.8
|
9.5
|
1.0
|
|
H
|
E:PHE63
|
4.9
|
10.0
|
1.0
|
|
C
|
E:ASP59
|
4.9
|
7.8
|
1.0
|
|
HA
|
E:ASP57
|
4.9
|
9.2
|
1.0
|
|
HB3
|
E:GLN61
|
4.9
|
12.7
|
1.0
|
|
HB3
|
E:ASP59
|
5.0
|
10.7
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5jt9
Go back to
Calcium Binding Sites List in 5jt9
Calcium binding site 3 out
of 4 in the Thermolysin in Complex with JC106.
 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 JC106. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca404
b:10.6
occ:1.00
|
O
|
E:ASN183
|
2.3
|
11.7
|
1.0
|
|
OE2
|
E:GLU190
|
2.3
|
8.9
|
1.0
|
|
O
|
E:HOH593
|
2.3
|
13.6
|
1.0
|
|
OD2
|
E:ASP185
|
2.3
|
10.1
|
1.0
|
|
O
|
E:HOH539
|
2.3
|
14.3
|
1.0
|
|
OE2
|
E:GLU177
|
2.4
|
8.5
|
1.0
|
|
CG
|
E:ASP185
|
3.2
|
8.5
|
1.0
|
|
CD
|
E:GLU177
|
3.2
|
7.3
|
1.0
|
|
CD
|
E:GLU190
|
3.3
|
7.9
|
1.0
|
|
C
|
E:ASN183
|
3.5
|
12.1
|
1.0
|
|
HA
|
E:PRO184
|
3.5
|
11.6
|
1.0
|
|
HG3
|
E:GLU190
|
3.6
|
10.7
|
1.0
|
|
OD1
|
E:ASP185
|
3.6
|
8.0
|
1.0
|
|
OE1
|
E:GLU177
|
3.7
|
7.9
|
1.0
|
|
HB2
|
E:ASN183
|
3.8
|
20.0
|
1.0
|
|
CA
|
E:CA402
|
3.8
|
7.3
|
1.0
|
|
HB3
|
E:ASN183
|
3.8
|
20.0
|
1.0
|
|
HG2
|
E:GLU190
|
3.8
|
10.7
|
1.0
|
|
CG
|
E:GLU190
|
3.9
|
8.9
|
1.0
|
|
H
|
E:ASP185
|
4.0
|
10.5
|
1.0
|
|
CA
|
E:PRO184
|
4.1
|
9.7
|
1.0
|
|
N
|
E:ASP185
|
4.1
|
8.8
|
1.0
|
|
CB
|
E:ASN183
|
4.2
|
16.6
|
1.0
|
|
OD2
|
E:ASP191
|
4.2
|
12.4
|
1.0
|
|
C
|
E:PRO184
|
4.2
|
9.8
|
1.0
|
|
CG
|
E:GLU177
|
4.3
|
7.4
|
1.0
|
|
HG2
|
E:GLU177
|
4.3
|
8.9
|
1.0
|
|
N
|
E:PRO184
|
4.3
|
10.7
|
1.0
|
|
OD1
|
E:ASP191
|
4.3
|
12.1
|
1.0
|
|
OE1
|
E:GLU190
|
4.3
|
8.2
|
1.0
|
|
HB3
|
E:ASP185
|
4.3
|
10.6
|
1.0
|
|
HG3
|
E:GLU177
|
4.3
|
8.9
|
1.0
|
|
CB
|
E:ASP185
|
4.4
|
8.8
|
1.0
|
|
O
|
E:LYS182
|
4.4
|
14.7
|
1.0
|
|
O
|
E:HOH616
|
4.5
|
28.8
|
0.5
|
|
CA
|
E:ASN183
|
4.5
|
14.5
|
1.0
|
|
CG
|
E:ASP191
|
4.6
|
10.8
|
1.0
|
|
O
|
E:HOH878
|
4.6
|
42.5
|
1.0
|
|
CA
|
E:ASP185
|
4.9
|
8.5
|
1.0
|
|
O
|
E:PRO184
|
4.9
|
11.2
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5jt9
Go back to
Calcium Binding Sites List in 5jt9
Calcium binding site 4 out
of 4 in the Thermolysin in Complex with JC106.
 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 JC106. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca405
b:10.3
occ:1.00
|
O
|
E:ILE197
|
2.3
|
14.8
|
1.0
|
|
OD1
|
E:ASP200
|
2.4
|
10.8
|
1.0
|
|
O
|
E:HOH769
|
2.4
|
17.3
|
1.0
|
|
O
|
E:TYR193
|
2.4
|
9.7
|
1.0
|
|
OG1
|
E:THR194
|
2.4
|
10.9
|
1.0
|
|
O
|
E:THR194
|
2.4
|
11.6
|
1.0
|
|
O
|
E:HOH596
|
2.4
|
13.5
|
1.0
|
|
C
|
E:THR194
|
3.2
|
11.0
|
1.0
|
|
C
|
E:TYR193
|
3.4
|
9.4
|
1.0
|
|
CG
|
E:ASP200
|
3.4
|
10.5
|
1.0
|
|
CB
|
E:THR194
|
3.5
|
11.0
|
1.0
|
|
HB
|
E:ILE197
|
3.5
|
21.2
|
1.0
|
|
C
|
E:ILE197
|
3.5
|
15.8
|
1.0
|
|
H
|
E:ILE197
|
3.6
|
19.3
|
1.0
|
|
CA
|
E:THR194
|
3.7
|
10.2
|
1.0
|
|
HB
|
E:THR194
|
3.7
|
13.2
|
1.0
|
|
OD2
|
E:ASP200
|
3.8
|
11.3
|
1.0
|
|
H
|
E:ASP200
|
3.9
|
15.3
|
1.0
|
|
N
|
E:THR194
|
3.9
|
9.8
|
1.0
|
|
HB3
|
E:TYR193
|
4.0
|
11.6
|
1.0
|
|
HD2
|
E:TYR193
|
4.0
|
13.5
|
1.0
|
|
HA
|
E:SER198
|
4.1
|
22.9
|
1.0
|
|
CA
|
E:ILE197
|
4.2
|
16.3
|
1.0
|
|
N
|
E:PRO195
|
4.3
|
12.0
|
1.0
|
|
CB
|
E:ILE197
|
4.3
|
17.6
|
1.0
|
|
HA
|
E:PRO195
|
4.3
|
16.4
|
1.0
|
|
N
|
E:ILE197
|
4.3
|
16.1
|
1.0
|
|
HG22
|
E:ILE197
|
4.4
|
21.4
|
1.0
|
|
O
|
E:HOH773
|
4.4
|
37.4
|
1.0
|
|
O
|
E:ASP200
|
4.5
|
10.8
|
1.0
|
|
N
|
E:SER198
|
4.5
|
17.4
|
1.0
|
|
O
|
E:HOH624
|
4.5
|
37.6
|
1.0
|
|
CA
|
E:TYR193
|
4.6
|
9.1
|
1.0
|
|
HA
|
E:THR194
|
4.6
|
12.2
|
1.0
|
|
N
|
E:ASP200
|
4.6
|
12.7
|
1.0
|
|
CA
|
E:PRO195
|
4.7
|
13.6
|
1.0
|
|
O
|
E:GLU190
|
4.7
|
9.6
|
1.0
|
|
CD2
|
E:TYR193
|
4.7
|
11.2
|
1.0
|
|
CB
|
E:TYR193
|
4.7
|
9.6
|
1.0
|
|
O
|
E:HOH798
|
4.7
|
25.9
|
1.0
|
|
CA
|
E:SER198
|
4.7
|
19.1
|
1.0
|
|
H
|
E:GLY199
|
4.7
|
19.9
|
1.0
|
|
CB
|
E:ASP200
|
4.7
|
11.2
|
1.0
|
|
CG2
|
E:THR194
|
4.7
|
10.9
|
1.0
|
|
H
|
E:THR194
|
4.8
|
11.7
|
1.0
|
|
C
|
E:ASP200
|
4.8
|
10.6
|
1.0
|
|
CG2
|
E:ILE197
|
4.9
|
17.8
|
1.0
|
|
HG23
|
E:THR194
|
4.9
|
13.1
|
1.0
|
|
CA
|
E:ASP200
|
4.9
|
11.5
|
1.0
|
|
H
|
E:TYR193
|
4.9
|
10.7
|
1.0
|
|
C
|
E:PRO195
|
4.9
|
15.2
|
1.0
|
|
C
|
E:SER198
|
5.0
|
18.0
|
1.0
|
|
N
|
E:GLY199
|
5.0
|
16.5
|
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: Mon Jul 15 06:33:50 2024
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