Calcium in PDB 6tli: Thermolysin (60% Isopropanol Soaked Crystals)
Enzymatic activity of Thermolysin (60% Isopropanol Soaked Crystals)
All present enzymatic activity of Thermolysin (60% Isopropanol Soaked Crystals):
3.4.24.27;
Protein crystallography data
The structure of Thermolysin (60% Isopropanol Soaked Crystals), PDB code: 6tli
was solved by
A.C.English,
S.H.Done,
C.R.Groom,
R.E.Hubbard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.10
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.120,
94.120,
130.680,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.8 /
22.2
|
Other elements in 6tli:
The structure of Thermolysin (60% Isopropanol Soaked Crystals) also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin (60% Isopropanol Soaked Crystals)
(pdb code 6tli). 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 (60% Isopropanol Soaked Crystals), PDB code: 6tli:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6tli
Go back to
Calcium Binding Sites List in 6tli
Calcium binding site 1 out
of 4 in the Thermolysin (60% Isopropanol Soaked Crystals)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Thermolysin (60% Isopropanol Soaked Crystals) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca322
b:23.7
occ:1.00
|
OD2
|
A:ASP138
|
2.6
|
18.0
|
1.0
|
O
|
A:GLU187
|
2.6
|
16.5
|
1.0
|
O
|
A:HOH1014
|
2.6
|
18.4
|
1.0
|
OE1
|
A:GLU177
|
2.6
|
18.8
|
1.0
|
OD1
|
A:ASP185
|
2.7
|
20.2
|
1.0
|
OE1
|
A:GLU190
|
2.7
|
17.6
|
1.0
|
OE2
|
A:GLU190
|
2.7
|
18.6
|
1.0
|
OE2
|
A:GLU177
|
3.0
|
21.9
|
1.0
|
CD
|
A:GLU190
|
3.1
|
25.0
|
1.0
|
CD
|
A:GLU177
|
3.2
|
20.7
|
1.0
|
CG
|
A:ASP138
|
3.5
|
27.3
|
1.0
|
CG
|
A:ASP185
|
3.6
|
26.7
|
1.0
|
C
|
A:GLU187
|
3.6
|
20.2
|
1.0
|
CA
|
A:CA323
|
3.8
|
25.9
|
1.0
|
OD2
|
A:ASP185
|
3.9
|
22.3
|
1.0
|
CB
|
A:ASP138
|
4.0
|
20.1
|
1.0
|
N
|
A:GLU187
|
4.2
|
23.9
|
1.0
|
CA
|
A:ILE188
|
4.3
|
15.0
|
1.0
|
O
|
A:ASP185
|
4.3
|
24.2
|
1.0
|
OD1
|
A:ASP138
|
4.3
|
19.1
|
1.0
|
N
|
A:ILE188
|
4.4
|
19.0
|
1.0
|
N
|
A:GLY189
|
4.4
|
13.7
|
1.0
|
CA
|
A:GLU187
|
4.4
|
23.8
|
1.0
|
CG
|
A:GLU190
|
4.6
|
17.7
|
1.0
|
CG
|
A:GLU177
|
4.7
|
19.4
|
1.0
|
CB
|
A:GLU187
|
4.7
|
21.8
|
1.0
|
C
|
A:ASP185
|
4.7
|
24.3
|
1.0
|
O
|
A:HOH1029
|
4.7
|
23.9
|
1.0
|
N
|
A:ASP185
|
4.7
|
20.1
|
1.0
|
C
|
A:ILE188
|
4.8
|
19.8
|
1.0
|
O
|
A:HOH1030
|
4.9
|
22.2
|
1.0
|
N
|
A:GLU190
|
4.9
|
17.7
|
1.0
|
CB
|
A:ASP185
|
5.0
|
19.1
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6tli
Go back to
Calcium Binding Sites List in 6tli
Calcium binding site 2 out
of 4 in the Thermolysin (60% Isopropanol Soaked Crystals)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Thermolysin (60% Isopropanol Soaked Crystals) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca323
b:25.9
occ:1.00
|
O
|
A:HOH1030
|
2.4
|
22.2
|
1.0
|
OD2
|
A:ASP185
|
2.5
|
22.3
|
1.0
|
O
|
A:HOH1013
|
2.6
|
22.4
|
1.0
|
OE2
|
A:GLU190
|
2.6
|
18.6
|
1.0
|
O
|
A:ASN183
|
2.6
|
21.5
|
1.0
|
OE2
|
A:GLU177
|
2.6
|
21.9
|
1.0
|
CD
|
A:GLU177
|
3.3
|
20.7
|
1.0
|
CG
|
A:ASP185
|
3.3
|
26.7
|
1.0
|
CD
|
A:GLU190
|
3.5
|
25.0
|
1.0
|
OD1
|
A:ASP185
|
3.7
|
20.2
|
1.0
|
OE1
|
A:GLU177
|
3.7
|
18.8
|
1.0
|
C
|
A:ASN183
|
3.7
|
27.9
|
1.0
|
O
|
A:LYS182
|
3.8
|
30.6
|
1.0
|
CA
|
A:CA322
|
3.8
|
23.7
|
1.0
|
N
|
A:ASP185
|
4.1
|
20.1
|
1.0
|
CG
|
A:GLU190
|
4.1
|
17.7
|
1.0
|
CB
|
A:ASN183
|
4.1
|
36.1
|
1.0
|
CA
|
A:PRO184
|
4.2
|
24.4
|
1.0
|
C
|
A:PRO184
|
4.2
|
26.3
|
1.0
|
OD1
|
A:ASP191
|
4.3
|
22.7
|
1.0
|
CG
|
A:GLU177
|
4.3
|
19.4
|
1.0
|
OE1
|
A:GLU190
|
4.4
|
17.6
|
1.0
|
OD2
|
A:ASP191
|
4.4
|
24.0
|
1.0
|
N
|
A:PRO184
|
4.4
|
27.6
|
1.0
|
CB
|
A:ASP185
|
4.5
|
19.1
|
1.0
|
CA
|
A:ASN183
|
4.6
|
24.0
|
1.0
|
CG
|
A:ASP191
|
4.7
|
22.6
|
1.0
|
CA
|
A:ASP185
|
4.9
|
18.1
|
1.0
|
O
|
A:PRO184
|
4.9
|
23.9
|
1.0
|
C
|
A:LYS182
|
4.9
|
30.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6tli
Go back to
Calcium Binding Sites List in 6tli
Calcium binding site 3 out
of 4 in the Thermolysin (60% Isopropanol Soaked Crystals)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Thermolysin (60% Isopropanol Soaked Crystals) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca324
b:26.6
occ:1.00
|
O
|
A:GLN61
|
2.4
|
21.3
|
1.0
|
O
|
A:HOH1016
|
2.4
|
35.4
|
1.0
|
O
|
A:HOH1027
|
2.5
|
18.5
|
1.0
|
OD1
|
A:ASP59
|
2.6
|
21.8
|
1.0
|
OD1
|
A:ASP57
|
2.6
|
18.8
|
1.0
|
O
|
A:HOH1047
|
2.6
|
33.4
|
1.0
|
OD2
|
A:ASP57
|
2.7
|
22.1
|
1.0
|
CG
|
A:ASP57
|
3.1
|
21.4
|
1.0
|
CG
|
A:ASP59
|
3.5
|
30.1
|
1.0
|
C
|
A:GLN61
|
3.5
|
23.2
|
1.0
|
OD2
|
A:ASP59
|
3.7
|
32.9
|
1.0
|
N
|
A:GLN61
|
3.9
|
21.6
|
1.0
|
O
|
A:HOH1052
|
4.0
|
38.9
|
1.0
|
CA
|
A:GLN61
|
4.2
|
27.9
|
1.0
|
N
|
A:ASP59
|
4.2
|
20.5
|
1.0
|
CB
|
A:GLN61
|
4.4
|
32.2
|
1.0
|
N
|
A:ASN60
|
4.6
|
24.1
|
1.0
|
CB
|
A:ASP57
|
4.6
|
12.4
|
1.0
|
O
|
A:HOH1009
|
4.6
|
20.8
|
1.0
|
OD2
|
A:ASP67
|
4.7
|
23.5
|
1.0
|
N
|
A:PHE62
|
4.7
|
21.2
|
1.0
|
CB
|
A:ASP59
|
4.7
|
15.1
|
1.0
|
CA
|
A:PHE62
|
4.7
|
19.9
|
1.0
|
O
|
A:HOH1044
|
4.8
|
29.0
|
1.0
|
CA
|
A:ASP59
|
4.8
|
20.9
|
1.0
|
N
|
A:ALA58
|
4.8
|
18.0
|
1.0
|
C
|
A:ASN60
|
4.9
|
24.9
|
1.0
|
C
|
A:ASP59
|
4.9
|
22.5
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6tli
Go back to
Calcium Binding Sites List in 6tli
Calcium binding site 4 out
of 4 in the Thermolysin (60% Isopropanol Soaked Crystals)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Thermolysin (60% Isopropanol Soaked Crystals) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca325
b:28.2
occ:1.00
|
O
|
A:ILE197
|
2.3
|
36.5
|
1.0
|
O
|
A:HOH1065
|
2.4
|
27.5
|
1.0
|
O
|
A:TYR193
|
2.4
|
24.8
|
1.0
|
O
|
A:HOH1038
|
2.5
|
26.9
|
1.0
|
OG1
|
A:THR194
|
2.6
|
30.4
|
1.0
|
OD1
|
A:ASP200
|
2.6
|
23.0
|
1.0
|
O
|
A:THR194
|
2.7
|
26.8
|
1.0
|
C
|
A:THR194
|
3.4
|
28.6
|
1.0
|
C
|
A:TYR193
|
3.4
|
20.5
|
1.0
|
C
|
A:ILE197
|
3.4
|
35.2
|
1.0
|
CG
|
A:ASP200
|
3.7
|
15.0
|
1.0
|
CB
|
A:THR194
|
3.7
|
32.3
|
1.0
|
OD2
|
A:ASP200
|
3.8
|
24.9
|
1.0
|
CA
|
A:THR194
|
3.9
|
24.1
|
1.0
|
N
|
A:THR194
|
4.1
|
23.2
|
1.0
|
CA
|
A:ILE197
|
4.2
|
39.3
|
1.0
|
CB
|
A:ILE197
|
4.2
|
40.8
|
1.0
|
N
|
A:ILE197
|
4.3
|
42.8
|
1.0
|
N
|
A:PRO195
|
4.3
|
29.1
|
1.0
|
N
|
A:SER198
|
4.5
|
31.1
|
1.0
|
O
|
A:ASP200
|
4.5
|
25.7
|
1.0
|
CA
|
A:TYR193
|
4.6
|
22.4
|
1.0
|
N
|
A:ASP200
|
4.6
|
26.0
|
1.0
|
CB
|
A:TYR193
|
4.6
|
22.4
|
1.0
|
O
|
A:GLU190
|
4.7
|
21.2
|
1.0
|
CA
|
A:SER198
|
4.7
|
32.9
|
1.0
|
CD2
|
A:TYR193
|
4.7
|
26.1
|
1.0
|
CA
|
A:PRO195
|
4.7
|
31.9
|
1.0
|
CB
|
A:ASP200
|
4.8
|
19.0
|
1.0
|
C
|
A:ASP200
|
4.9
|
22.2
|
1.0
|
C
|
A:SER198
|
4.9
|
32.6
|
1.0
|
CG2
|
A:ILE197
|
4.9
|
35.4
|
1.0
|
CG2
|
A:THR194
|
5.0
|
28.6
|
1.0
|
C
|
A:PRO195
|
5.0
|
34.5
|
1.0
|
CG
|
A:TYR193
|
5.0
|
27.4
|
1.0
|
|
Reference:
A.C.English,
S.H.Done,
L.S.Caves,
C.R.Groom,
R.E.Hubbard.
Locating Interaction Sites on Proteins: the Crystal Structure of Thermolysin Soaked in 2% to 100% Isopropanol. Proteins V. 37 628 1999.
ISSN: ISSN 0887-3585
PubMed: 10651278
DOI: 10.1002/(SICI)1097-0134(19991201)37:4<628::AID-PROT13>3.3.CO;2-7
Page generated: Tue Jul 16 15:20:44 2024
|