Calcium in PDB 1kr6: Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid)
Enzymatic activity of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid)
All present enzymatic activity of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid):
3.4.24.27;
Protein crystallography data
The structure of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid), PDB code: 1kr6
was solved by
M.Senda,
T.Senda,
S.Kidokoro,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
1.80
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.772,
93.772,
131.359,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.2 /
18.1
|
Other elements in 1kr6:
The structure of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid)
(pdb code 1kr6). 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 Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid), PDB code: 1kr6:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1kr6
Go back to
Calcium Binding Sites List in 1kr6
Calcium binding site 1 out
of 4 in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:10.8
occ:1.00
|
O
|
A:GLU187
|
2.4
|
10.7
|
1.0
|
O
|
A:HOH1320
|
2.4
|
11.5
|
1.0
|
OD2
|
A:ASP138
|
2.4
|
12.5
|
1.0
|
OE1
|
A:GLU177
|
2.4
|
11.4
|
1.0
|
OE1
|
A:GLU190
|
2.5
|
11.7
|
1.0
|
OD1
|
A:ASP185
|
2.5
|
12.1
|
1.0
|
OE2
|
A:GLU190
|
2.6
|
11.5
|
1.0
|
OE2
|
A:GLU177
|
2.8
|
12.0
|
1.0
|
CD
|
A:GLU190
|
2.8
|
10.8
|
1.0
|
CD
|
A:GLU177
|
2.9
|
13.1
|
1.0
|
C
|
A:GLU187
|
3.4
|
11.6
|
1.0
|
CG
|
A:ASP138
|
3.5
|
11.9
|
1.0
|
CG
|
A:ASP185
|
3.6
|
14.3
|
1.0
|
CA
|
A:CA402
|
3.8
|
12.7
|
1.0
|
OD2
|
A:ASP185
|
3.9
|
14.2
|
1.0
|
CB
|
A:ASP138
|
4.0
|
10.4
|
1.0
|
N
|
A:GLU187
|
4.2
|
14.4
|
1.0
|
O
|
A:ASP185
|
4.2
|
13.3
|
1.0
|
N
|
A:ILE188
|
4.3
|
11.7
|
1.0
|
CA
|
A:GLU187
|
4.3
|
13.9
|
1.0
|
CA
|
A:ILE188
|
4.3
|
11.8
|
1.0
|
CG
|
A:GLU190
|
4.3
|
12.0
|
1.0
|
OD1
|
A:ASP138
|
4.4
|
12.6
|
1.0
|
CG
|
A:GLU177
|
4.4
|
11.1
|
1.0
|
O
|
A:HOH1416
|
4.4
|
29.1
|
1.0
|
N
|
A:GLY189
|
4.5
|
12.3
|
1.0
|
O
|
A:HOH1358
|
4.6
|
16.5
|
1.0
|
CB
|
A:GLU187
|
4.6
|
16.2
|
1.0
|
C
|
A:ASP185
|
4.7
|
13.8
|
1.0
|
C
|
A:ILE188
|
4.8
|
11.8
|
1.0
|
CB
|
A:ASP185
|
4.8
|
14.1
|
1.0
|
N
|
A:ASP185
|
4.9
|
14.4
|
1.0
|
O
|
A:HOH1345
|
4.9
|
16.1
|
1.0
|
N
|
A:GLU190
|
4.9
|
11.6
|
1.0
|
CB
|
A:GLU177
|
4.9
|
11.2
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1kr6
Go back to
Calcium Binding Sites List in 1kr6
Calcium binding site 2 out
of 4 in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:12.7
occ:1.00
|
OE2
|
A:GLU190
|
2.3
|
11.5
|
1.0
|
OD2
|
A:ASP185
|
2.3
|
14.2
|
1.0
|
O
|
A:ASN183
|
2.4
|
15.6
|
1.0
|
O
|
A:HOH1334
|
2.4
|
16.0
|
1.0
|
OE2
|
A:GLU177
|
2.4
|
12.0
|
1.0
|
O
|
A:HOH1345
|
2.4
|
16.1
|
1.0
|
CG
|
A:ASP185
|
3.2
|
14.3
|
1.0
|
CD
|
A:GLU190
|
3.2
|
10.8
|
1.0
|
CD
|
A:GLU177
|
3.3
|
13.1
|
1.0
|
C
|
A:ASN183
|
3.5
|
18.4
|
1.0
|
OD1
|
A:ASP185
|
3.6
|
12.1
|
1.0
|
CG
|
A:GLU190
|
3.8
|
12.0
|
1.0
|
CA
|
A:CA401
|
3.8
|
10.8
|
1.0
|
OE1
|
A:GLU177
|
3.8
|
11.4
|
1.0
|
O
|
A:LYS182
|
3.9
|
24.6
|
1.0
|
OD2
|
A:ASP191
|
4.2
|
16.4
|
1.0
|
N
|
A:ASP185
|
4.2
|
14.4
|
1.0
|
OE1
|
A:GLU190
|
4.2
|
11.7
|
1.0
|
CA
|
A:PRO184
|
4.2
|
16.9
|
1.0
|
CG
|
A:GLU177
|
4.3
|
11.1
|
1.0
|
CB
|
A:ASN183
|
4.3
|
22.8
|
1.0
|
N
|
A:PRO184
|
4.3
|
18.2
|
1.0
|
C
|
A:PRO184
|
4.3
|
17.4
|
1.0
|
OD1
|
A:ASP191
|
4.3
|
16.4
|
1.0
|
CB
|
A:ASP185
|
4.4
|
14.1
|
1.0
|
CA
|
A:ASN183
|
4.5
|
20.5
|
1.0
|
CG
|
A:ASP191
|
4.6
|
16.5
|
1.0
|
O
|
A:HOH1416
|
4.7
|
29.1
|
1.0
|
CA
|
A:ASP185
|
4.9
|
13.9
|
1.0
|
C
|
A:LYS182
|
4.9
|
23.9
|
1.0
|
O
|
A:PRO184
|
5.0
|
16.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1kr6
Go back to
Calcium Binding Sites List in 1kr6
Calcium binding site 3 out
of 4 in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:11.5
occ:1.00
|
O
|
A:GLN61
|
2.3
|
11.9
|
1.0
|
O
|
A:HOH1331
|
2.3
|
13.7
|
1.0
|
OD1
|
A:ASP57
|
2.4
|
12.2
|
1.0
|
OD1
|
A:ASP59
|
2.4
|
14.1
|
1.0
|
O
|
A:HOH1329
|
2.5
|
12.6
|
1.0
|
OD2
|
A:ASP57
|
2.5
|
14.0
|
1.0
|
O
|
A:HOH1336
|
2.5
|
17.1
|
1.0
|
CG
|
A:ASP57
|
2.8
|
12.9
|
1.0
|
CG
|
A:ASP59
|
3.4
|
16.7
|
1.0
|
C
|
A:GLN61
|
3.5
|
11.7
|
1.0
|
OD2
|
A:ASP59
|
3.8
|
16.6
|
1.0
|
N
|
A:GLN61
|
4.0
|
11.6
|
1.0
|
O
|
A:HOH1370
|
4.1
|
22.9
|
1.0
|
CA
|
A:GLN61
|
4.2
|
12.9
|
1.0
|
CB
|
A:ASP57
|
4.3
|
11.1
|
1.0
|
N
|
A:ASP59
|
4.3
|
13.7
|
1.0
|
CB
|
A:GLN61
|
4.4
|
15.8
|
1.0
|
N
|
A:PHE62
|
4.5
|
11.4
|
1.0
|
O
|
A:HOH1318
|
4.6
|
11.2
|
1.0
|
O
|
A:HOH1340
|
4.6
|
16.2
|
1.0
|
OD2
|
A:ASP67
|
4.7
|
11.1
|
1.0
|
CB
|
A:ASP59
|
4.7
|
14.9
|
1.0
|
CA
|
A:PHE62
|
4.7
|
10.6
|
1.0
|
N
|
A:ASN60
|
4.7
|
13.0
|
1.0
|
O
|
A:HOH1418
|
4.7
|
35.8
|
1.0
|
N
|
A:ALA58
|
4.7
|
11.6
|
1.0
|
CA
|
A:ASP59
|
4.8
|
13.6
|
1.0
|
C
|
A:ASP59
|
4.9
|
14.4
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1kr6
Go back to
Calcium Binding Sites List in 1kr6
Calcium binding site 4 out
of 4 in the Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Thermolysin Complexed with Z-D-Glutamic Acid (Benzyloxycarbonyl-D- Glutamic Acid) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:14.9
occ:1.00
|
O
|
A:ILE197
|
2.2
|
28.2
|
1.0
|
O
|
A:TYR193
|
2.3
|
13.4
|
1.0
|
OD1
|
A:ASP200
|
2.4
|
16.1
|
1.0
|
OG1
|
A:THR194
|
2.4
|
17.5
|
1.0
|
O
|
A:THR194
|
2.4
|
20.3
|
1.0
|
O
|
A:HOH1324
|
2.4
|
17.0
|
1.0
|
O
|
A:HOH1366
|
2.5
|
22.4
|
1.0
|
C
|
A:THR194
|
3.2
|
19.6
|
1.0
|
C
|
A:TYR193
|
3.3
|
15.7
|
1.0
|
C
|
A:ILE197
|
3.4
|
29.8
|
1.0
|
CG
|
A:ASP200
|
3.4
|
16.5
|
1.0
|
CB
|
A:THR194
|
3.4
|
17.0
|
1.0
|
CA
|
A:THR194
|
3.7
|
18.1
|
1.0
|
OD2
|
A:ASP200
|
3.7
|
18.5
|
1.0
|
N
|
A:THR194
|
3.9
|
16.4
|
1.0
|
CA
|
A:ILE197
|
4.1
|
29.2
|
1.0
|
CB
|
A:ILE197
|
4.2
|
29.4
|
1.0
|
N
|
A:ILE197
|
4.2
|
29.4
|
1.0
|
N
|
A:PRO195
|
4.2
|
21.0
|
1.0
|
N
|
A:SER198
|
4.4
|
29.8
|
1.0
|
O
|
A:ASP200
|
4.4
|
17.9
|
1.0
|
CA
|
A:SER198
|
4.5
|
30.6
|
1.0
|
CA
|
A:TYR193
|
4.5
|
14.8
|
1.0
|
O
|
A:GLU190
|
4.6
|
13.2
|
1.0
|
O
|
A:HOH1382
|
4.6
|
30.9
|
1.0
|
N
|
A:ASP200
|
4.6
|
20.9
|
1.0
|
CA
|
A:PRO195
|
4.7
|
22.9
|
1.0
|
CB
|
A:TYR193
|
4.7
|
15.6
|
1.0
|
CD2
|
A:TYR193
|
4.7
|
20.1
|
1.0
|
CG2
|
A:THR194
|
4.7
|
19.2
|
1.0
|
CB
|
A:ASP200
|
4.7
|
17.6
|
1.0
|
C
|
A:ASP200
|
4.8
|
17.0
|
1.0
|
CG2
|
A:ILE197
|
4.9
|
27.8
|
1.0
|
C
|
A:PRO195
|
5.0
|
25.1
|
1.0
|
C
|
A:SER198
|
5.0
|
29.3
|
1.0
|
CA
|
A:ASP200
|
5.0
|
18.5
|
1.0
|
|
Reference:
M.Senda,
T.Senda,
S.Kidokoro.
Crystal Structure Analyses of Thermolysin in Complex with Its Inhibitors. To Be Published.
Page generated: Thu Jul 11 11:26:54 2024
|