Calcium in PDB 3do2: Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline
Enzymatic activity of Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline
All present enzymatic activity of Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline, PDB code: 3do2
was solved by
E.Pechkova,
S.K.Tripathi,
C.Nicolini,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
68.04 /
1.22
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.562,
92.562,
128.712,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23.8 /
26.1
|
Other elements in 3do2:
The structure of Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline
(pdb code 3do2). 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 By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline, PDB code: 3do2:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 3do2
Go back to
Calcium Binding Sites List in 3do2
Calcium binding site 1 out
of 4 in the Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:12.6
occ:1.00
|
O
|
A:GLU187
|
2.3
|
14.4
|
1.0
|
OD2
|
A:ASP138
|
2.4
|
11.9
|
1.0
|
O
|
A:HOH1005
|
2.4
|
10.8
|
1.0
|
OD1
|
A:ASP185
|
2.5
|
14.2
|
1.0
|
OE1
|
A:GLU177
|
2.5
|
11.0
|
1.0
|
OE2
|
A:GLU190
|
2.5
|
15.9
|
1.0
|
OE1
|
A:GLU190
|
2.6
|
12.0
|
1.0
|
OE2
|
A:GLU177
|
2.7
|
12.5
|
1.0
|
CD
|
A:GLU190
|
2.9
|
14.8
|
1.0
|
CD
|
A:GLU177
|
2.9
|
13.0
|
1.0
|
CG
|
A:ASP138
|
3.4
|
13.7
|
1.0
|
C
|
A:GLU187
|
3.4
|
15.8
|
1.0
|
CG
|
A:ASP185
|
3.5
|
15.4
|
1.0
|
CA
|
A:CA402
|
3.8
|
17.4
|
1.0
|
OD2
|
A:ASP185
|
3.8
|
16.0
|
1.0
|
CB
|
A:ASP138
|
4.0
|
12.8
|
1.0
|
O
|
A:ASP185
|
4.2
|
14.6
|
1.0
|
O
|
A:HOH1143
|
4.2
|
30.5
|
1.0
|
N
|
A:GLU187
|
4.2
|
15.7
|
1.0
|
N
|
A:ILE188
|
4.2
|
15.0
|
1.0
|
CA
|
A:GLU187
|
4.3
|
15.9
|
1.0
|
OD1
|
A:ASP138
|
4.3
|
13.8
|
1.0
|
CA
|
A:ILE188
|
4.3
|
14.5
|
1.0
|
O
|
A:HOH1043
|
4.3
|
17.6
|
1.0
|
CG
|
A:GLU190
|
4.4
|
14.6
|
1.0
|
CG
|
A:GLU177
|
4.4
|
12.7
|
1.0
|
N
|
A:GLY189
|
4.5
|
12.4
|
1.0
|
C
|
A:ASP185
|
4.6
|
15.8
|
1.0
|
CB
|
A:GLU187
|
4.6
|
18.2
|
1.0
|
N
|
A:ASP185
|
4.7
|
15.4
|
1.0
|
CB
|
A:ASP185
|
4.8
|
15.2
|
1.0
|
C
|
A:ILE188
|
4.8
|
14.0
|
1.0
|
O
|
A:HOH1030
|
4.9
|
19.0
|
1.0
|
CB
|
A:GLU177
|
4.9
|
12.6
|
1.0
|
CA
|
A:ASP185
|
5.0
|
14.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 3do2
Go back to
Calcium Binding Sites List in 3do2
Calcium binding site 2 out
of 4 in the Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:17.4
occ:1.00
|
O
|
A:ASN183
|
2.3
|
17.8
|
1.0
|
OE2
|
A:GLU177
|
2.3
|
12.5
|
1.0
|
O
|
A:HOH1030
|
2.3
|
19.0
|
1.0
|
OE2
|
A:GLU190
|
2.4
|
15.9
|
1.0
|
OD2
|
A:ASP185
|
2.4
|
16.0
|
1.0
|
O
|
A:HOH1019
|
2.5
|
21.1
|
1.0
|
CD
|
A:GLU177
|
3.2
|
13.0
|
1.0
|
CG
|
A:ASP185
|
3.2
|
15.4
|
1.0
|
CD
|
A:GLU190
|
3.3
|
14.8
|
1.0
|
C
|
A:ASN183
|
3.5
|
18.6
|
1.0
|
OD1
|
A:ASP185
|
3.6
|
14.2
|
1.0
|
OE1
|
A:GLU177
|
3.8
|
11.0
|
1.0
|
CA
|
A:CA401
|
3.8
|
12.6
|
1.0
|
CG
|
A:GLU190
|
3.9
|
14.6
|
1.0
|
CA
|
A:PRO184
|
4.1
|
15.7
|
1.0
|
OD2
|
A:ASP191
|
4.1
|
15.3
|
1.0
|
OD1
|
A:ASP191
|
4.2
|
16.7
|
1.0
|
N
|
A:ASP185
|
4.2
|
15.4
|
1.0
|
C
|
A:PRO184
|
4.2
|
16.0
|
1.0
|
CG
|
A:GLU177
|
4.2
|
12.7
|
1.0
|
CB
|
A:ASN183
|
4.3
|
21.6
|
1.0
|
N
|
A:PRO184
|
4.3
|
16.9
|
1.0
|
OE1
|
A:GLU190
|
4.3
|
12.0
|
1.0
|
O
|
A:HOH1143
|
4.3
|
30.5
|
1.0
|
CB
|
A:ASP185
|
4.4
|
15.2
|
1.0
|
O
|
A:LYS182
|
4.4
|
23.9
|
1.0
|
CG
|
A:ASP191
|
4.5
|
16.1
|
1.0
|
CA
|
A:ASN183
|
4.5
|
20.7
|
1.0
|
O
|
A:PRO184
|
4.8
|
16.7
|
1.0
|
CA
|
A:ASP185
|
4.9
|
14.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 3do2
Go back to
Calcium Binding Sites List in 3do2
Calcium binding site 3 out
of 4 in the Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:13.8
occ:1.00
|
O
|
A:HOH1021
|
2.2
|
16.0
|
1.0
|
O
|
A:GLN61
|
2.3
|
11.0
|
1.0
|
O
|
A:HOH1016
|
2.3
|
12.5
|
1.0
|
OD1
|
A:ASP57
|
2.4
|
14.8
|
1.0
|
O
|
A:HOH1014
|
2.4
|
12.7
|
1.0
|
OD1
|
A:ASP59
|
2.5
|
13.8
|
1.0
|
OD2
|
A:ASP57
|
2.6
|
13.8
|
1.0
|
CG
|
A:ASP57
|
2.8
|
14.4
|
1.0
|
CG
|
A:ASP59
|
3.5
|
15.3
|
1.0
|
C
|
A:GLN61
|
3.5
|
13.0
|
1.0
|
OD2
|
A:ASP59
|
3.8
|
15.0
|
1.0
|
O
|
A:HOH1055
|
3.9
|
17.7
|
1.0
|
N
|
A:GLN61
|
4.0
|
13.6
|
1.0
|
CA
|
A:GLN61
|
4.2
|
13.9
|
1.0
|
CB
|
A:GLN61
|
4.3
|
16.5
|
1.0
|
CB
|
A:ASP57
|
4.3
|
13.6
|
1.0
|
N
|
A:ASP59
|
4.4
|
13.8
|
1.0
|
O
|
A:HOH1025
|
4.5
|
15.1
|
1.0
|
O
|
A:HOH1133
|
4.5
|
21.8
|
1.0
|
N
|
A:PHE62
|
4.5
|
12.0
|
1.0
|
OD2
|
A:ASP67
|
4.6
|
13.7
|
1.0
|
O
|
A:HOH1003
|
4.7
|
12.2
|
1.0
|
N
|
A:ASN60
|
4.7
|
12.0
|
1.0
|
CB
|
A:ASP59
|
4.7
|
14.1
|
1.0
|
N
|
A:ALA58
|
4.7
|
12.7
|
1.0
|
CA
|
A:PHE62
|
4.8
|
12.9
|
1.0
|
CA
|
A:ASP59
|
4.8
|
13.4
|
1.0
|
C
|
A:ASP59
|
4.9
|
13.3
|
1.0
|
O
|
A:HOH1154
|
4.9
|
26.7
|
1.0
|
|
Calcium binding site 4 out
of 4 in 3do2
Go back to
Calcium Binding Sites List in 3do2
Calcium binding site 4 out
of 4 in the Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Thermolysin By Lb Nanotemplate Method After High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:16.3
occ:1.00
|
O
|
A:ILE197
|
2.3
|
21.8
|
1.0
|
O
|
A:TYR193
|
2.4
|
15.4
|
1.0
|
O
|
A:HOH1009
|
2.4
|
14.4
|
1.0
|
OD1
|
A:ASP200
|
2.4
|
16.3
|
1.0
|
OG1
|
A:THR194
|
2.5
|
16.7
|
1.0
|
O
|
A:THR194
|
2.5
|
17.2
|
1.0
|
O
|
A:HOH1051
|
2.6
|
23.3
|
1.0
|
C
|
A:THR194
|
3.3
|
18.0
|
1.0
|
C
|
A:TYR193
|
3.3
|
16.5
|
1.0
|
CB
|
A:THR194
|
3.5
|
17.8
|
1.0
|
C
|
A:ILE197
|
3.5
|
23.7
|
1.0
|
CG
|
A:ASP200
|
3.5
|
17.6
|
1.0
|
CA
|
A:THR194
|
3.6
|
17.4
|
1.0
|
OD2
|
A:ASP200
|
3.9
|
17.9
|
1.0
|
N
|
A:THR194
|
3.9
|
15.9
|
1.0
|
CB
|
A:ILE197
|
4.2
|
23.1
|
1.0
|
CA
|
A:ILE197
|
4.2
|
23.2
|
1.0
|
N
|
A:ILE197
|
4.3
|
23.9
|
1.0
|
N
|
A:PRO195
|
4.4
|
19.2
|
1.0
|
O
|
A:ASP200
|
4.4
|
17.8
|
1.0
|
O
|
A:HOH1067
|
4.4
|
29.3
|
1.0
|
N
|
A:SER198
|
4.5
|
24.1
|
1.0
|
CA
|
A:TYR193
|
4.5
|
16.0
|
1.0
|
O
|
A:GLU190
|
4.6
|
14.9
|
1.0
|
N
|
A:ASP200
|
4.6
|
19.9
|
1.0
|
CB
|
A:TYR193
|
4.7
|
18.1
|
1.0
|
CA
|
A:SER198
|
4.7
|
24.5
|
1.0
|
CD2
|
A:TYR193
|
4.8
|
19.0
|
1.0
|
CG2
|
A:THR194
|
4.8
|
18.0
|
1.0
|
CB
|
A:ASP200
|
4.8
|
17.6
|
1.0
|
C
|
A:ASP200
|
4.8
|
18.1
|
1.0
|
CA
|
A:PRO195
|
4.8
|
20.6
|
1.0
|
CG2
|
A:ILE197
|
4.8
|
23.1
|
1.0
|
CA
|
A:ASP200
|
5.0
|
18.4
|
1.0
|
C
|
A:SER198
|
5.0
|
24.2
|
1.0
|
N
|
A:GLY199
|
5.0
|
23.6
|
1.0
|
|
Reference:
E.Pechkova,
S.K.Tripathi,
C.Nicolini.
Radiation Damage in Protein Structural Characterization By Synchrotron Radiation: State of the Art and Nanotechnology-Based Perspective To Be Published.
Page generated: Sat Jul 13 09:05:36 2024
|