Calcium in PDB 2zrq: Crystal Structure of S324A-Subtilisin
Enzymatic activity of Crystal Structure of S324A-Subtilisin
All present enzymatic activity of Crystal Structure of S324A-Subtilisin:
3.4.21.62;
Protein crystallography data
The structure of Crystal Structure of S324A-Subtilisin, PDB code: 2zrq
was solved by
S.Tanaka,
Y.Takeuchi,
H.Matsumura,
Y.Koga,
K.Takano,
S.Kanaya,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.81 /
2.16
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.188,
60.925,
92.277,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.4 /
19.7
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of S324A-Subtilisin
(pdb code 2zrq). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Crystal Structure of S324A-Subtilisin, PDB code: 2zrq:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 2zrq
Go back to
Calcium Binding Sites List in 2zrq
Calcium binding site 1 out
of 7 in the Crystal Structure of S324A-Subtilisin
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of S324A-Subtilisin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1
b:19.5
occ:1.00
|
O
|
A:VAL170
|
2.2
|
13.3
|
1.0
|
OE1
|
A:GLN84
|
2.3
|
16.9
|
1.0
|
O
|
A:LEU164
|
2.4
|
17.6
|
1.0
|
O
|
A:ILE168
|
2.4
|
17.6
|
1.0
|
OD1
|
A:ASN166
|
2.4
|
18.3
|
1.0
|
OD1
|
A:ASP124
|
2.5
|
16.5
|
1.0
|
OD2
|
A:ASP124
|
2.6
|
20.4
|
1.0
|
CG
|
A:ASP124
|
2.9
|
18.9
|
1.0
|
CG
|
A:ASN166
|
3.4
|
21.7
|
1.0
|
C
|
A:VAL170
|
3.4
|
13.6
|
1.0
|
CD
|
A:GLN84
|
3.5
|
18.2
|
1.0
|
C
|
A:LEU164
|
3.5
|
17.4
|
1.0
|
C
|
A:ILE168
|
3.5
|
18.1
|
1.0
|
N
|
A:VAL170
|
3.8
|
14.6
|
1.0
|
ND2
|
A:ASN166
|
3.9
|
18.5
|
1.0
|
N
|
A:ASN166
|
4.0
|
21.3
|
1.0
|
CG
|
A:GLN84
|
4.1
|
21.4
|
1.0
|
CA
|
A:VAL170
|
4.2
|
13.5
|
1.0
|
C
|
A:GLY169
|
4.3
|
15.2
|
1.0
|
N
|
A:ILE168
|
4.3
|
20.8
|
1.0
|
N
|
A:LEU164
|
4.3
|
15.8
|
1.0
|
CA
|
A:LEU164
|
4.4
|
17.2
|
1.0
|
N
|
A:VAL171
|
4.4
|
13.4
|
1.0
|
CA
|
A:ILE168
|
4.4
|
19.6
|
1.0
|
CG1
|
A:ILE168
|
4.4
|
19.3
|
1.0
|
CB
|
A:ASP124
|
4.4
|
18.4
|
1.0
|
N
|
A:ASN165
|
4.4
|
18.6
|
1.0
|
N
|
A:GLY169
|
4.5
|
17.3
|
1.0
|
NE2
|
A:GLN84
|
4.6
|
15.8
|
1.0
|
CA
|
A:ASN165
|
4.6
|
19.1
|
1.0
|
CA
|
A:VAL171
|
4.6
|
14.2
|
1.0
|
CA
|
A:GLY169
|
4.6
|
16.1
|
1.0
|
CB
|
A:ASN166
|
4.6
|
21.2
|
1.0
|
CB
|
A:GLN84
|
4.6
|
22.9
|
1.0
|
CA
|
A:ASN166
|
4.6
|
22.0
|
1.0
|
O
|
A:ASN166
|
4.7
|
22.4
|
1.0
|
C
|
A:ASN166
|
4.7
|
22.8
|
1.0
|
CB
|
A:LEU164
|
4.7
|
17.4
|
1.0
|
C
|
A:ASN165
|
4.7
|
20.6
|
1.0
|
CB
|
A:VAL171
|
4.8
|
14.6
|
1.0
|
C
|
A:ALA163
|
4.8
|
14.2
|
1.0
|
O
|
A:GLY169
|
5.0
|
14.7
|
1.0
|
|
Calcium binding site 2 out
of 7 in 2zrq
Go back to
Calcium Binding Sites List in 2zrq
Calcium binding site 2 out
of 7 in the Crystal Structure of S324A-Subtilisin
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of S324A-Subtilisin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca5
b:14.9
occ:1.00
|
O
|
A:ALA227
|
2.3
|
13.7
|
1.0
|
O
|
A:VAL108
|
2.4
|
14.1
|
1.0
|
OE1
|
A:GLN110
|
2.4
|
11.9
|
1.0
|
OE1
|
A:GLU229
|
2.5
|
16.2
|
1.0
|
O
|
A:HOH444
|
2.5
|
15.1
|
1.0
|
O
|
A:HOH448
|
2.5
|
11.4
|
1.0
|
OE2
|
A:GLU229
|
2.7
|
15.3
|
1.0
|
CD
|
A:GLU229
|
3.0
|
15.6
|
1.0
|
CD
|
A:GLN110
|
3.5
|
17.5
|
1.0
|
C
|
A:VAL108
|
3.6
|
14.6
|
1.0
|
C
|
A:ALA227
|
3.6
|
14.3
|
1.0
|
NE2
|
A:GLN110
|
4.1
|
16.7
|
1.0
|
CG2
|
A:VAL108
|
4.2
|
12.8
|
1.0
|
N
|
A:ALA227
|
4.2
|
14.8
|
1.0
|
N
|
A:GLN110
|
4.3
|
13.1
|
1.0
|
C
|
A:ASP226
|
4.3
|
16.4
|
1.0
|
CG
|
A:GLU229
|
4.4
|
11.5
|
1.0
|
CA
|
A:VAL108
|
4.5
|
14.3
|
1.0
|
CA
|
A:ALA227
|
4.5
|
14.4
|
1.0
|
O
|
A:ASP225
|
4.5
|
15.6
|
1.0
|
N
|
A:ILE109
|
4.5
|
13.9
|
1.0
|
N
|
A:ALA228
|
4.5
|
13.9
|
1.0
|
CA
|
A:ILE109
|
4.5
|
12.9
|
1.0
|
CA
|
A:ASP226
|
4.6
|
16.0
|
1.0
|
CA
|
A:ALA228
|
4.6
|
14.5
|
1.0
|
C
|
A:ALA228
|
4.6
|
14.5
|
1.0
|
C
|
A:ILE109
|
4.7
|
12.8
|
1.0
|
O
|
A:ASP226
|
4.7
|
17.2
|
1.0
|
N
|
A:GLY221
|
4.7
|
17.1
|
1.0
|
N
|
A:GLU229
|
4.8
|
14.1
|
1.0
|
CG
|
A:GLN110
|
4.8
|
12.5
|
1.0
|
O
|
A:ASP222
|
4.8
|
14.2
|
1.0
|
CB
|
A:GLN110
|
4.9
|
13.6
|
1.0
|
CB
|
A:VAL108
|
5.0
|
14.3
|
1.0
|
|
Calcium binding site 3 out
of 7 in 2zrq
Go back to
Calcium Binding Sites List in 2zrq
Calcium binding site 3 out
of 7 in the Crystal Structure of S324A-Subtilisin
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of S324A-Subtilisin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca7
b:26.4
occ:1.00
|
OD2
|
A:ASP119
|
2.3
|
20.2
|
1.0
|
OD1
|
A:ASP121
|
2.4
|
24.6
|
1.0
|
OD2
|
A:ASP314
|
2.4
|
24.6
|
1.0
|
OD1
|
A:ASP315
|
2.5
|
28.1
|
1.0
|
O
|
A:HOH467
|
2.8
|
23.0
|
1.0
|
O
|
A:HOH421
|
3.0
|
31.3
|
1.0
|
OD1
|
A:ASP119
|
3.0
|
17.8
|
1.0
|
CG
|
A:ASP119
|
3.0
|
17.5
|
1.0
|
CG
|
A:ASP121
|
3.4
|
22.0
|
1.0
|
CG
|
A:ASP314
|
3.6
|
23.7
|
1.0
|
CG
|
A:ASP315
|
3.6
|
25.6
|
1.0
|
OD2
|
A:ASP121
|
3.7
|
26.9
|
1.0
|
N
|
A:ASP315
|
4.0
|
22.0
|
1.0
|
O
|
A:HOH486
|
4.0
|
29.9
|
1.0
|
OD2
|
A:ASP315
|
4.1
|
29.1
|
1.0
|
OD1
|
A:ASP314
|
4.2
|
25.9
|
1.0
|
N
|
A:HIS122
|
4.2
|
16.9
|
1.0
|
C
|
A:ASP121
|
4.3
|
18.0
|
1.0
|
CA
|
A:HIS122
|
4.5
|
16.6
|
1.0
|
CB
|
A:ASP119
|
4.5
|
17.3
|
1.0
|
O
|
A:ASP121
|
4.5
|
17.2
|
1.0
|
C
|
A:ASP314
|
4.6
|
22.2
|
1.0
|
CA
|
A:ASP314
|
4.6
|
21.9
|
1.0
|
CB
|
A:ASP121
|
4.6
|
18.6
|
1.0
|
CB
|
A:ASP314
|
4.7
|
21.9
|
1.0
|
N
|
A:ASP121
|
4.7
|
18.6
|
1.0
|
CB
|
A:ASP315
|
4.7
|
22.8
|
1.0
|
CA
|
A:ASP121
|
4.7
|
18.7
|
1.0
|
CA
|
A:ASP315
|
4.8
|
22.3
|
1.0
|
|
Calcium binding site 4 out
of 7 in 2zrq
Go back to
Calcium Binding Sites List in 2zrq
Calcium binding site 4 out
of 7 in the Crystal Structure of S324A-Subtilisin
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of S324A-Subtilisin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2
b:19.6
occ:1.00
|
O
|
A:VAL210
|
2.1
|
17.6
|
1.0
|
O
|
A:LEU205
|
2.1
|
18.1
|
1.0
|
OD2
|
A:ASP226
|
2.2
|
15.5
|
1.0
|
OD1
|
A:ASP208
|
2.2
|
16.9
|
1.0
|
O
|
A:HOH492
|
2.4
|
10.9
|
1.0
|
O
|
A:HOH433
|
2.4
|
14.8
|
1.0
|
CG
|
A:ASP208
|
3.1
|
17.9
|
1.0
|
C
|
A:VAL210
|
3.3
|
18.7
|
1.0
|
C
|
A:LEU205
|
3.3
|
18.0
|
1.0
|
OD2
|
A:ASP208
|
3.3
|
15.6
|
1.0
|
CG
|
A:ASP226
|
3.3
|
17.7
|
1.0
|
N
|
A:VAL210
|
3.8
|
18.6
|
1.0
|
OD1
|
A:ASP226
|
3.8
|
21.1
|
1.0
|
N
|
A:ASP226
|
3.9
|
15.7
|
1.0
|
CA
|
A:VAL210
|
4.1
|
19.2
|
1.0
|
CA
|
A:LEU205
|
4.1
|
17.6
|
1.0
|
O
|
A:ALA211
|
4.2
|
17.4
|
1.0
|
N
|
A:GLY206
|
4.2
|
17.6
|
1.0
|
CA
|
A:GLY206
|
4.3
|
18.2
|
1.0
|
N
|
A:ALA211
|
4.3
|
17.9
|
1.0
|
OD1
|
A:ASP225
|
4.3
|
19.5
|
1.0
|
CA
|
A:ALA211
|
4.4
|
19.0
|
1.0
|
N
|
A:ALA227
|
4.4
|
14.8
|
1.0
|
O
|
A:ILE204
|
4.4
|
16.1
|
1.0
|
C
|
A:ASP226
|
4.5
|
16.4
|
1.0
|
CB
|
A:ASP226
|
4.5
|
16.1
|
1.0
|
CA
|
A:ASP226
|
4.5
|
16.0
|
1.0
|
CB
|
A:ASP208
|
4.5
|
18.0
|
1.0
|
C
|
A:ALA211
|
4.5
|
18.3
|
1.0
|
C
|
A:GLY206
|
4.6
|
18.5
|
1.0
|
N
|
A:GLY209
|
4.6
|
18.6
|
1.0
|
CB
|
A:VAL210
|
4.6
|
19.6
|
1.0
|
N
|
A:ASP208
|
4.6
|
18.6
|
1.0
|
O
|
A:GLY206
|
4.7
|
18.4
|
1.0
|
CA
|
A:ASP208
|
4.8
|
18.6
|
1.0
|
C
|
A:GLY209
|
4.9
|
18.6
|
1.0
|
C
|
A:ASP208
|
4.9
|
18.9
|
1.0
|
CB
|
A:ASP225
|
4.9
|
15.4
|
1.0
|
|
Calcium binding site 5 out
of 7 in 2zrq
Go back to
Calcium Binding Sites List in 2zrq
Calcium binding site 5 out
of 7 in the Crystal Structure of S324A-Subtilisin
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of S324A-Subtilisin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca3
b:16.4
occ:1.00
|
OD1
|
A:ASP222
|
2.2
|
15.9
|
1.0
|
OD2
|
A:ASP225
|
2.2
|
17.4
|
1.0
|
O
|
A:ILE218
|
2.3
|
19.5
|
1.0
|
OD1
|
A:ASP212
|
2.4
|
17.4
|
1.0
|
OD2
|
A:ASP214
|
2.4
|
18.0
|
1.0
|
OD1
|
A:ASP216
|
2.4
|
18.0
|
1.0
|
CG
|
A:ASP222
|
3.3
|
15.8
|
1.0
|
CG
|
A:ASP216
|
3.3
|
16.9
|
1.0
|
CG
|
A:ASP225
|
3.5
|
17.4
|
1.0
|
CG
|
A:ASP214
|
3.5
|
19.9
|
1.0
|
C
|
A:ILE218
|
3.5
|
19.0
|
1.0
|
CG
|
A:ASP212
|
3.5
|
18.9
|
1.0
|
OD2
|
A:ASP216
|
3.7
|
19.4
|
1.0
|
OD1
|
A:ASP214
|
3.9
|
19.2
|
1.0
|
CB
|
A:ASP222
|
4.0
|
14.8
|
1.0
|
N
|
A:ILE218
|
4.0
|
18.7
|
1.0
|
CA
|
A:ILE218
|
4.2
|
19.8
|
1.0
|
CA
|
A:CA4
|
4.2
|
24.9
|
1.0
|
OD1
|
A:ASP225
|
4.3
|
19.5
|
1.0
|
CA
|
A:ASP212
|
4.3
|
19.4
|
1.0
|
OD2
|
A:ASP212
|
4.3
|
21.9
|
1.0
|
N
|
A:ASP216
|
4.3
|
19.4
|
1.0
|
OD2
|
A:ASP222
|
4.3
|
15.8
|
1.0
|
CB
|
A:ASP212
|
4.4
|
18.9
|
1.0
|
CB
|
A:ASP225
|
4.4
|
15.4
|
1.0
|
N
|
A:ILE219
|
4.5
|
18.8
|
1.0
|
CB
|
A:ILE218
|
4.5
|
19.2
|
1.0
|
CB
|
A:ASP216
|
4.5
|
18.1
|
1.0
|
C
|
A:ASP212
|
4.6
|
20.5
|
1.0
|
N
|
A:ASP214
|
4.6
|
20.2
|
1.0
|
N
|
A:LYS213
|
4.7
|
21.2
|
1.0
|
N
|
A:GLY215
|
4.8
|
19.8
|
1.0
|
CA
|
A:ILE219
|
4.8
|
18.4
|
1.0
|
CB
|
A:ASP214
|
4.8
|
19.8
|
1.0
|
N
|
A:GLY217
|
4.8
|
18.3
|
1.0
|
CA
|
A:ASP216
|
4.8
|
18.8
|
1.0
|
C
|
A:ASP216
|
5.0
|
18.5
|
1.0
|
|
Calcium binding site 6 out
of 7 in 2zrq
Go back to
Calcium Binding Sites List in 2zrq
Calcium binding site 6 out
of 7 in the Crystal Structure of S324A-Subtilisin
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of S324A-Subtilisin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4
b:24.9
occ:1.00
|
OD2
|
A:ASP216
|
2.3
|
19.4
|
1.0
|
O
|
A:HOH548
|
2.4
|
28.5
|
1.0
|
OD1
|
A:ASP214
|
2.4
|
19.2
|
1.0
|
OD2
|
A:ASP222
|
2.5
|
15.8
|
1.0
|
OD2
|
A:ASP224
|
2.5
|
21.5
|
1.0
|
O
|
A:HOH489
|
2.6
|
37.0
|
1.0
|
OD1
|
A:ASP222
|
2.7
|
15.9
|
1.0
|
CG
|
A:ASP222
|
2.9
|
15.8
|
1.0
|
CG
|
A:ASP216
|
3.3
|
16.9
|
1.0
|
CG
|
A:ASP224
|
3.5
|
21.0
|
1.0
|
CG
|
A:ASP214
|
3.5
|
19.9
|
1.0
|
CB
|
A:ASP224
|
3.6
|
17.2
|
1.0
|
OD2
|
A:ASP214
|
3.9
|
18.0
|
1.0
|
OD1
|
A:ASP216
|
4.0
|
18.0
|
1.0
|
CA
|
A:CA3
|
4.2
|
16.4
|
1.0
|
O
|
A:HOH517
|
4.3
|
32.4
|
1.0
|
CB
|
A:ASP216
|
4.3
|
18.1
|
1.0
|
CB
|
A:ASP222
|
4.3
|
14.8
|
1.0
|
O
|
A:HOH561
|
4.4
|
33.7
|
1.0
|
N
|
A:ASP224
|
4.6
|
17.1
|
1.0
|
OD1
|
A:ASP224
|
4.7
|
24.0
|
1.0
|
CA
|
A:ASP224
|
4.7
|
17.9
|
1.0
|
CB
|
A:ASP214
|
4.8
|
19.8
|
1.0
|
|
Calcium binding site 7 out
of 7 in 2zrq
Go back to
Calcium Binding Sites List in 2zrq
Calcium binding site 7 out
of 7 in the Crystal Structure of S324A-Subtilisin
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of S324A-Subtilisin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca6
b:15.9
occ:1.00
|
OD1
|
A:ASP372
|
2.2
|
17.6
|
1.0
|
OD1
|
A:ASP379
|
2.2
|
13.7
|
1.0
|
O
|
A:PRO375
|
2.2
|
17.4
|
1.0
|
O
|
A:LEU373
|
2.3
|
17.3
|
1.0
|
O
|
A:GLY377
|
2.4
|
18.2
|
1.0
|
O
|
A:HOH416
|
2.5
|
11.6
|
1.0
|
CG
|
A:ASP379
|
3.4
|
15.1
|
1.0
|
CG
|
A:ASP372
|
3.4
|
20.6
|
1.0
|
C
|
A:PRO375
|
3.5
|
17.2
|
1.0
|
C
|
A:LEU373
|
3.5
|
17.5
|
1.0
|
C
|
A:GLY377
|
3.6
|
18.1
|
1.0
|
N
|
A:GLY377
|
3.8
|
18.9
|
1.0
|
C
|
A:GLY374
|
4.0
|
15.4
|
1.0
|
OD2
|
A:ASP372
|
4.0
|
24.5
|
1.0
|
N
|
A:LEU373
|
4.1
|
19.1
|
1.0
|
O
|
A:GLY374
|
4.1
|
15.2
|
1.0
|
CB
|
A:ASP379
|
4.1
|
15.5
|
1.0
|
C
|
A:THR376
|
4.1
|
18.7
|
1.0
|
O
|
A:GLY383
|
4.1
|
14.7
|
1.0
|
N
|
A:PRO375
|
4.1
|
15.1
|
1.0
|
C
|
A:ASP372
|
4.3
|
18.8
|
1.0
|
CA
|
A:GLY377
|
4.3
|
18.7
|
1.0
|
OD2
|
A:ASP379
|
4.3
|
17.1
|
1.0
|
N
|
A:THR376
|
4.4
|
17.3
|
1.0
|
N
|
A:ASP379
|
4.4
|
15.9
|
1.0
|
CA
|
A:THR376
|
4.4
|
18.4
|
1.0
|
CA
|
A:PRO375
|
4.4
|
16.0
|
1.0
|
CA
|
A:GLY374
|
4.4
|
16.3
|
1.0
|
N
|
A:GLY374
|
4.4
|
16.4
|
1.0
|
CA
|
A:LEU373
|
4.5
|
18.2
|
1.0
|
CA
|
A:ASP372
|
4.5
|
18.9
|
1.0
|
CB
|
A:ASP372
|
4.6
|
18.9
|
1.0
|
C
|
A:TRP378
|
4.6
|
17.1
|
1.0
|
N
|
A:TRP378
|
4.6
|
17.5
|
1.0
|
O
|
A:THR376
|
4.6
|
18.6
|
1.0
|
CD
|
A:PRO375
|
4.8
|
15.5
|
1.0
|
O
|
A:ASP372
|
4.8
|
20.8
|
1.0
|
CA
|
A:TRP378
|
4.8
|
17.1
|
1.0
|
O
|
A:HOH585
|
4.8
|
29.2
|
1.0
|
CA
|
A:ASP379
|
4.9
|
15.7
|
1.0
|
CB
|
A:PRO375
|
5.0
|
15.2
|
1.0
|
O
|
A:HOH538
|
5.0
|
27.3
|
1.0
|
|
Reference:
S.Tanaka,
Y.Takeuchi,
H.Matsumura,
Y.Koga,
K.Takano,
S.Kanaya.
Crystal Structure of Tk-Subtilisin Folded Without Propeptide: Requirement of Propeptide For Acceleration of Folding Febs Lett. V. 582 3875 2008.
ISSN: ISSN 0014-5793
PubMed: 18951896
DOI: 10.1016/J.FEBSLET.2008.10.025
Page generated: Sat Jul 13 06:50:49 2024
|