Calcium in PDB 5fsj: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure
Enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure
All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure:
3.4.24.27;
Protein crystallography data
The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure, PDB code: 5fsj
was solved by
B.Lafumat,
C.Mueller-Dieckmann,
N.Colloc'h,
T.Prange,
A.Royant,
P.Van Derlinden,
P.Carpentier,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.46 /
1.20
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.922,
92.922,
130.252,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
10.4 /
12.2
|
Other elements in 5fsj:
The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure
(pdb code 5fsj). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure, PDB code: 5fsj:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 5fsj
Go back to
Calcium Binding Sites List in 5fsj
Calcium binding site 1 out
of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1003
b:15.3
occ:1.00
|
O
|
A:ILE197
|
2.3
|
26.5
|
1.0
|
O
|
A:TYR193
|
2.4
|
14.3
|
1.0
|
OD1
|
A:ASP200
|
2.4
|
16.4
|
1.0
|
O
|
A:THR194
|
2.4
|
16.9
|
1.0
|
O
|
A:HOH2371
|
2.4
|
16.5
|
1.0
|
OG1
|
A:THR194
|
2.4
|
15.9
|
1.0
|
O
|
A:HOH2375
|
2.4
|
21.6
|
1.0
|
HG1
|
A:THR194
|
2.8
|
19.1
|
0.0
|
C
|
A:THR194
|
3.2
|
16.5
|
1.0
|
C
|
A:TYR193
|
3.4
|
13.8
|
1.0
|
CG
|
A:ASP200
|
3.4
|
17.1
|
1.0
|
HB
|
A:ILE197
|
3.5
|
41.3
|
1.0
|
C
|
A:ILE197
|
3.5
|
27.6
|
1.0
|
CB
|
A:THR194
|
3.5
|
16.8
|
1.0
|
H
|
A:ILE197
|
3.6
|
34.7
|
1.0
|
CA
|
A:THR194
|
3.7
|
15.9
|
1.0
|
HB
|
A:THR194
|
3.7
|
20.1
|
1.0
|
OD2
|
A:ASP200
|
3.8
|
19.1
|
1.0
|
H
|
A:ASP200
|
3.9
|
23.5
|
1.0
|
N
|
A:THR194
|
3.9
|
13.8
|
1.0
|
HA
|
A:SER198
|
4.1
|
38.8
|
1.0
|
HD2
|
A:TYR193
|
4.1
|
19.2
|
1.0
|
HB3
|
A:TYR193
|
4.1
|
16.9
|
1.0
|
CA
|
A:ILE197
|
4.2
|
31.2
|
1.0
|
CB
|
A:ILE197
|
4.2
|
34.4
|
1.0
|
N
|
A:ILE197
|
4.3
|
28.9
|
1.0
|
N
|
A:PRO195
|
4.3
|
18.6
|
1.0
|
HA
|
A:PRO195
|
4.3
|
24.4
|
1.0
|
HG23
|
A:ILE197
|
4.4
|
36.0
|
1.0
|
O
|
A:HOH2382
|
4.4
|
42.7
|
1.0
|
O
|
A:ASP200
|
4.5
|
16.4
|
1.0
|
N
|
A:SER198
|
4.5
|
29.0
|
1.0
|
O
|
A:HOH2378
|
4.5
|
42.0
|
1.0
|
CA
|
A:TYR193
|
4.6
|
12.1
|
1.0
|
HA
|
A:THR194
|
4.6
|
19.0
|
1.0
|
O
|
A:GLU190
|
4.6
|
12.9
|
1.0
|
N
|
A:ASP200
|
4.6
|
19.6
|
1.0
|
O
|
A:HOH2373
|
4.6
|
27.8
|
1.0
|
CA
|
A:SER198
|
4.7
|
32.3
|
1.0
|
O
|
A:HOH2370
|
4.7
|
39.2
|
1.0
|
CA
|
A:PRO195
|
4.7
|
20.4
|
1.0
|
CD2
|
A:TYR193
|
4.7
|
16.0
|
1.0
|
CB
|
A:TYR193
|
4.7
|
14.1
|
1.0
|
H
|
A:THR194
|
4.7
|
16.6
|
1.0
|
CB
|
A:ASP200
|
4.7
|
17.2
|
1.0
|
H
|
A:GLY199
|
4.7
|
29.3
|
1.0
|
CG2
|
A:THR194
|
4.8
|
17.3
|
1.0
|
C
|
A:ASP200
|
4.8
|
16.2
|
1.0
|
CG2
|
A:ILE197
|
4.9
|
29.9
|
1.0
|
HG21
|
A:THR194
|
4.9
|
20.7
|
1.0
|
H
|
A:TYR193
|
4.9
|
14.1
|
1.0
|
C
|
A:PRO195
|
4.9
|
27.0
|
1.0
|
CA
|
A:ASP200
|
5.0
|
18.0
|
1.0
|
C
|
A:SER198
|
5.0
|
27.9
|
1.0
|
|
Calcium binding site 2 out
of 5 in 5fsj
Go back to
Calcium Binding Sites List in 5fsj
Calcium binding site 2 out
of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1004
b:12.2
occ:0.69
|
OE2
|
A:GLU190
|
2.3
|
11.5
|
1.0
|
O
|
A:ASN183
|
2.3
|
15.7
|
1.0
|
O
|
A:HOH2353
|
2.3
|
23.0
|
1.0
|
O
|
A:HOH2361
|
2.4
|
18.1
|
1.0
|
OD2
|
A:ASP185
|
2.4
|
14.2
|
1.0
|
OE2
|
A:GLU177
|
2.6
|
12.4
|
1.0
|
CG
|
A:ASP185
|
3.2
|
12.3
|
1.0
|
CD
|
A:GLU190
|
3.3
|
10.7
|
1.0
|
CD
|
A:GLU177
|
3.3
|
10.4
|
1.0
|
HG3
|
A:GLU190
|
3.5
|
14.7
|
1.0
|
C
|
A:ASN183
|
3.5
|
15.5
|
1.0
|
HA
|
A:PRO184
|
3.5
|
15.7
|
1.0
|
OD1
|
A:ASP185
|
3.6
|
11.7
|
1.0
|
HB2
|
A:ASN183
|
3.7
|
25.7
|
1.0
|
OE1
|
A:GLU177
|
3.7
|
11.4
|
1.0
|
HG2
|
A:GLU190
|
3.7
|
14.7
|
1.0
|
CG
|
A:GLU190
|
3.8
|
12.2
|
1.0
|
CA
|
A:CA1009
|
3.8
|
10.6
|
1.0
|
O
|
A:HOH2365
|
3.9
|
46.5
|
1.0
|
H
|
A:ASP185
|
4.0
|
14.1
|
1.0
|
CA
|
A:PRO184
|
4.1
|
13.1
|
1.0
|
HB3
|
A:ASN183
|
4.1
|
25.7
|
1.0
|
N
|
A:ASP185
|
4.1
|
11.8
|
1.0
|
OD1
|
A:ASP191
|
4.2
|
16.1
|
1.0
|
O
|
A:HOH2360
|
4.2
|
26.4
|
1.0
|
C
|
A:PRO184
|
4.2
|
13.0
|
1.0
|
CB
|
A:ASN183
|
4.3
|
21.4
|
1.0
|
OD2
|
A:ASP191
|
4.3
|
15.1
|
1.0
|
OE1
|
A:GLU190
|
4.3
|
11.5
|
1.0
|
N
|
A:PRO184
|
4.3
|
13.8
|
1.0
|
CG
|
A:GLU177
|
4.3
|
10.9
|
1.0
|
HB3
|
A:ASP185
|
4.3
|
14.4
|
1.0
|
HG2
|
A:GLU177
|
4.3
|
13.1
|
1.0
|
CB
|
A:ASP185
|
4.4
|
12.0
|
1.0
|
H
|
A:ASN183
|
4.4
|
27.5
|
1.0
|
HG3
|
A:GLU177
|
4.4
|
13.1
|
1.0
|
O
|
A:HOH2316
|
4.5
|
26.4
|
1.0
|
O
|
A:HOH2178
|
4.5
|
52.5
|
1.0
|
CA
|
A:ASN183
|
4.5
|
18.7
|
1.0
|
CG
|
A:ASP191
|
4.5
|
13.8
|
1.0
|
O
|
A:LYS182
|
4.7
|
24.2
|
0.6
|
CA
|
A:ASP185
|
4.9
|
12.4
|
1.0
|
O
|
A:HOH2364
|
4.9
|
40.2
|
1.0
|
O
|
A:PRO184
|
4.9
|
15.9
|
1.0
|
O
|
A:HOH2317
|
5.0
|
17.8
|
1.0
|
|
Calcium binding site 3 out
of 5 in 5fsj
Go back to
Calcium Binding Sites List in 5fsj
Calcium binding site 3 out
of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1005
b:22.4
occ:0.69
|
CA
|
A:CA1010
|
2.4
|
10.8
|
1.0
|
O
|
A:HOH2545
|
2.7
|
27.8
|
1.0
|
OD2
|
A:ASP59
|
2.8
|
15.9
|
1.0
|
OD1
|
A:ASP59
|
3.0
|
11.5
|
1.0
|
O
|
A:HOH2179
|
3.0
|
17.2
|
1.0
|
O
|
A:HOH2172
|
3.1
|
11.7
|
1.0
|
O
|
A:HOH2171
|
3.2
|
13.8
|
1.0
|
CG
|
A:ASP59
|
3.2
|
11.8
|
1.0
|
HB2
|
A:GLN61
|
3.2
|
14.9
|
1.0
|
O
|
A:GLN61
|
3.5
|
10.8
|
1.0
|
O
|
A:HOH2176
|
3.5
|
30.1
|
0.3
|
O
|
A:HOH2546
|
3.6
|
24.4
|
1.0
|
O
|
A:HOH2077
|
4.1
|
33.4
|
1.0
|
CB
|
A:GLN61
|
4.2
|
12.4
|
1.0
|
C
|
A:GLN61
|
4.3
|
9.8
|
1.0
|
H
|
A:GLN61
|
4.4
|
12.2
|
1.0
|
O
|
A:HOH2078
|
4.4
|
16.3
|
1.0
|
HB3
|
A:GLN61
|
4.5
|
14.9
|
1.0
|
OD2
|
A:ASP57
|
4.7
|
10.8
|
1.0
|
CB
|
A:ASP59
|
4.7
|
11.9
|
1.0
|
O
|
A:HOH2183
|
4.7
|
24.0
|
1.0
|
O
|
A:HOH2086
|
4.7
|
30.0
|
1.0
|
H
|
A:PHE63
|
4.7
|
12.7
|
1.0
|
OD1
|
A:ASP57
|
4.7
|
10.6
|
1.0
|
CA
|
A:GLN61
|
4.8
|
10.7
|
1.0
|
HB3
|
A:ASP59
|
4.9
|
14.2
|
1.0
|
H
|
A:ASP59
|
4.9
|
13.0
|
1.0
|
|
Calcium binding site 4 out
of 5 in 5fsj
Go back to
Calcium Binding Sites List in 5fsj
Calcium binding site 4 out
of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1009
b:10.6
occ:1.00
|
O
|
A:GLU187
|
2.3
|
11.1
|
1.0
|
OD2
|
A:ASP138
|
2.4
|
10.9
|
1.0
|
O
|
A:HOH2318
|
2.4
|
11.8
|
1.0
|
OD1
|
A:ASP185
|
2.5
|
11.7
|
1.0
|
OE2
|
A:GLU190
|
2.5
|
11.5
|
1.0
|
OE1
|
A:GLU177
|
2.5
|
11.4
|
1.0
|
OE1
|
A:GLU190
|
2.5
|
11.5
|
1.0
|
OE2
|
A:GLU177
|
2.7
|
12.4
|
1.0
|
CD
|
A:GLU190
|
2.8
|
10.7
|
1.0
|
CD
|
A:GLU177
|
2.9
|
10.4
|
1.0
|
CG
|
A:ASP138
|
3.4
|
10.5
|
1.0
|
C
|
A:GLU187
|
3.4
|
11.5
|
1.0
|
CG
|
A:ASP185
|
3.5
|
12.3
|
1.0
|
HB3
|
A:ASP138
|
3.6
|
11.5
|
1.0
|
HA
|
A:ILE188
|
3.7
|
12.1
|
1.0
|
H
|
A:GLU187
|
3.7
|
14.1
|
1.0
|
CA
|
A:CA1004
|
3.8
|
12.2
|
0.7
|
H
|
A:GLY189
|
3.8
|
12.3
|
1.0
|
OD2
|
A:ASP185
|
3.8
|
14.2
|
1.0
|
HB2
|
A:GLU187
|
3.8
|
17.6
|
1.0
|
CB
|
A:ASP138
|
4.0
|
9.6
|
1.0
|
O
|
A:ASP185
|
4.1
|
11.8
|
1.0
|
H
|
A:ASP185
|
4.1
|
14.1
|
1.0
|
H
|
A:GLU190
|
4.2
|
12.8
|
1.0
|
N
|
A:GLU187
|
4.2
|
11.7
|
1.0
|
N
|
A:ILE188
|
4.2
|
11.0
|
1.0
|
O
|
A:HOH2316
|
4.2
|
26.4
|
1.0
|
OD1
|
A:ASP138
|
4.3
|
12.4
|
1.0
|
HB2
|
A:ASP138
|
4.3
|
11.5
|
1.0
|
CA
|
A:GLU187
|
4.3
|
12.4
|
1.0
|
HD11
|
A:ILE188
|
4.3
|
16.7
|
1.0
|
CG
|
A:GLU190
|
4.3
|
12.2
|
1.0
|
CA
|
A:ILE188
|
4.3
|
10.1
|
1.0
|
O
|
A:HOH2317
|
4.4
|
17.8
|
1.0
|
CG
|
A:GLU177
|
4.4
|
10.9
|
1.0
|
N
|
A:GLY189
|
4.4
|
10.2
|
1.0
|
CB
|
A:GLU187
|
4.5
|
14.7
|
1.0
|
C
|
A:ASP185
|
4.5
|
11.3
|
1.0
|
HG3
|
A:GLU190
|
4.6
|
14.7
|
1.0
|
HB2
|
A:GLU177
|
4.7
|
12.6
|
1.0
|
N
|
A:ASP185
|
4.7
|
11.8
|
1.0
|
O
|
A:HOH2353
|
4.8
|
23.0
|
1.0
|
CB
|
A:ASP185
|
4.8
|
12.0
|
1.0
|
HB3
|
A:GLU177
|
4.8
|
12.6
|
1.0
|
HG2
|
A:GLU190
|
4.8
|
14.7
|
1.0
|
HG2
|
A:GLU177
|
4.8
|
13.1
|
1.0
|
C
|
A:ILE188
|
4.8
|
10.4
|
1.0
|
HA
|
A:THR174
|
4.9
|
10.9
|
1.0
|
HG3
|
A:GLU177
|
4.9
|
13.1
|
1.0
|
CB
|
A:GLU177
|
4.9
|
10.4
|
1.0
|
CA
|
A:ASP185
|
4.9
|
12.4
|
1.0
|
HB3
|
A:GLU187
|
5.0
|
17.6
|
1.0
|
HB3
|
A:GLU190
|
5.0
|
14.4
|
1.0
|
N
|
A:GLU190
|
5.0
|
10.6
|
1.0
|
|
Calcium binding site 5 out
of 5 in 5fsj
Go back to
Calcium Binding Sites List in 5fsj
Calcium binding site 5 out
of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1010
b:10.8
occ:1.00
|
O
|
A:GLN61
|
2.3
|
10.8
|
1.0
|
O
|
A:HOH2171
|
2.3
|
13.8
|
1.0
|
OD2
|
A:ASP57
|
2.4
|
10.8
|
1.0
|
CA
|
A:CA1005
|
2.4
|
22.4
|
0.7
|
OD1
|
A:ASP59
|
2.4
|
11.5
|
1.0
|
O
|
A:HOH2172
|
2.4
|
11.7
|
1.0
|
OD1
|
A:ASP57
|
2.6
|
10.6
|
1.0
|
CG
|
A:ASP57
|
2.8
|
10.4
|
1.0
|
H
|
A:GLN61
|
3.3
|
12.2
|
1.0
|
CG
|
A:ASP59
|
3.4
|
11.8
|
1.0
|
C
|
A:GLN61
|
3.4
|
9.8
|
1.0
|
H
|
A:ASP59
|
3.5
|
13.0
|
1.0
|
HB2
|
A:GLN61
|
3.6
|
14.9
|
1.0
|
OD2
|
A:ASP59
|
3.8
|
15.9
|
1.0
|
N
|
A:GLN61
|
4.0
|
10.2
|
1.0
|
O
|
A:HOH2179
|
4.0
|
17.2
|
1.0
|
HA
|
A:PHE62
|
4.0
|
11.0
|
1.0
|
CA
|
A:GLN61
|
4.1
|
10.7
|
1.0
|
H
|
A:ALA58
|
4.3
|
12.5
|
1.0
|
CB
|
A:ASP57
|
4.3
|
10.6
|
1.0
|
N
|
A:ASP59
|
4.3
|
10.8
|
1.0
|
CB
|
A:GLN61
|
4.3
|
12.4
|
1.0
|
H
|
A:ASN60
|
4.4
|
12.3
|
1.0
|
O
|
A:HOH2174
|
4.5
|
14.5
|
1.0
|
N
|
A:PHE62
|
4.5
|
9.3
|
1.0
|
O
|
A:HOH2078
|
4.5
|
16.3
|
1.0
|
CB
|
A:ASP59
|
4.6
|
11.9
|
1.0
|
OD2
|
A:ASP67
|
4.6
|
10.5
|
1.0
|
N
|
A:ASN60
|
4.7
|
10.2
|
1.0
|
O
|
A:HOH2167
|
4.7
|
10.5
|
1.0
|
O
|
A:HOH2077
|
4.7
|
33.4
|
1.0
|
HB2
|
A:ASP57
|
4.7
|
12.7
|
1.0
|
O
|
A:HOH2545
|
4.7
|
27.8
|
1.0
|
N
|
A:ALA58
|
4.7
|
10.4
|
1.0
|
CA
|
A:PHE62
|
4.8
|
9.2
|
1.0
|
HB3
|
A:ASP57
|
4.8
|
12.7
|
1.0
|
CA
|
A:ASP59
|
4.8
|
11.4
|
1.0
|
H
|
A:PHE63
|
4.8
|
12.7
|
1.0
|
HA
|
A:ASP57
|
4.9
|
11.8
|
1.0
|
C
|
A:ASP59
|
4.9
|
10.9
|
1.0
|
HB3
|
A:GLN61
|
4.9
|
14.9
|
1.0
|
HB3
|
A:ASP59
|
5.0
|
14.2
|
1.0
|
|
Reference:
B.Lafumat,
C.Mueller-Dieckmann,
N.Colloc'h,
T.Prange,
A.Royant,
P.Van Der Linden,
P.Carpentier.
Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using A Novel `Soak-and-Freeze' Methodology. J.Appl.Crystallogr. V. 49 1478 2016.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576716010992
Page generated: Sun Jul 14 19:19:25 2024
|