Calcium in PDB 6qg9: Crystal Structure of Ideonella Sakaiensis Mhetase
Enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase
All present enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase:
3.1.1.102;
Protein crystallography data
The structure of Crystal Structure of Ideonella Sakaiensis Mhetase, PDB code: 6qg9
was solved by
G.J.Palm,
L.Reisky,
D.Boettcher,
H.Mueller,
E.A.P.Michels,
C.Walczak,
L.Berndt,
M.S.Weiss,
U.T.Bornscheuer,
G.Weber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
40.00 /
2.05
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.286,
137.949,
137.051,
83.01,
66.88,
68.45
|
|
R / Rfree (%)
|
21 /
26.2
|
Other elements in 6qg9:
The structure of Crystal Structure of Ideonella Sakaiensis Mhetase also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Ideonella Sakaiensis Mhetase
(pdb code 6qg9). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Ideonella Sakaiensis Mhetase, PDB code: 6qg9:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 1 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 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 Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:31.5
occ:1.00
|
O
|
A:LEU309
|
2.2
|
30.8
|
1.0
|
|
OD1
|
A:ASP311
|
2.4
|
31.6
|
1.0
|
|
OD2
|
A:ASP307
|
2.4
|
24.0
|
1.0
|
|
OD1
|
A:ASP307
|
2.5
|
29.4
|
1.0
|
|
O
|
A:ILE313
|
2.5
|
29.3
|
1.0
|
|
O
|
A:ASP304
|
2.5
|
24.4
|
1.0
|
|
OD1
|
A:ASP304
|
2.6
|
34.1
|
1.0
|
|
CG
|
A:ASP307
|
2.8
|
27.2
|
1.0
|
|
CG
|
A:ASP311
|
3.3
|
31.4
|
1.0
|
|
C
|
A:LEU309
|
3.5
|
33.7
|
1.0
|
|
OD2
|
A:ASP311
|
3.6
|
31.4
|
1.0
|
|
C
|
A:ASP304
|
3.6
|
30.3
|
1.0
|
|
C
|
A:ILE313
|
3.7
|
27.7
|
1.0
|
|
CG
|
A:ASP304
|
3.8
|
34.4
|
1.0
|
|
N
|
A:ASP311
|
3.9
|
33.4
|
1.0
|
|
OD2
|
A:ASP315
|
4.1
|
44.6
|
1.0
|
|
O
|
A:HOH924
|
4.2
|
22.0
|
1.0
|
|
CA
|
A:ASP304
|
4.3
|
30.4
|
1.0
|
|
CB
|
A:ASP307
|
4.3
|
26.2
|
1.0
|
|
N
|
A:ILE313
|
4.3
|
22.5
|
1.0
|
|
N
|
A:ALA310
|
4.4
|
33.7
|
1.0
|
|
CA
|
A:LEU309
|
4.4
|
31.8
|
1.0
|
|
CA
|
A:ILE313
|
4.4
|
26.0
|
1.0
|
|
CA
|
A:ALA310
|
4.4
|
35.2
|
1.0
|
|
CB
|
A:ASP311
|
4.5
|
30.2
|
1.0
|
|
N
|
A:LEU309
|
4.5
|
32.0
|
1.0
|
|
CB
|
A:ILE313
|
4.5
|
27.0
|
1.0
|
|
CB
|
A:LEU309
|
4.6
|
28.1
|
1.0
|
|
N
|
A:ASP315
|
4.6
|
25.1
|
1.0
|
|
C
|
A:ALA310
|
4.7
|
36.6
|
1.0
|
|
N
|
A:ALA305
|
4.7
|
32.4
|
1.0
|
|
OD2
|
A:ASP304
|
4.7
|
39.1
|
1.0
|
|
CA
|
A:ASP311
|
4.7
|
32.6
|
1.0
|
|
CB
|
A:ASP304
|
4.7
|
28.0
|
1.0
|
|
N
|
A:VAL314
|
4.7
|
24.4
|
1.0
|
|
CA
|
A:VAL314
|
4.9
|
26.0
|
1.0
|
|
N
|
A:ASP307
|
4.9
|
25.1
|
1.0
|
|
CA
|
A:ALA305
|
4.9
|
28.5
|
1.0
|
|
Calcium binding site 2 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 2 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 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 Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca701
b:21.6
occ:1.00
|
O
|
B:HOH924
|
2.2
|
25.6
|
1.0
|
|
OD1
|
B:ASP304
|
2.3
|
33.8
|
1.0
|
|
O
|
B:LEU309
|
2.4
|
26.0
|
1.0
|
|
O
|
B:ILE313
|
2.4
|
24.9
|
1.0
|
|
O
|
B:ASP304
|
2.5
|
33.8
|
1.0
|
|
OD1
|
B:ASP311
|
2.5
|
27.4
|
1.0
|
|
OD1
|
B:ASP307
|
2.7
|
30.0
|
1.0
|
|
OD2
|
B:ASP307
|
2.7
|
28.4
|
1.0
|
|
CG
|
B:ASP307
|
3.1
|
27.8
|
1.0
|
|
C
|
B:ASP304
|
3.4
|
25.1
|
1.0
|
|
CG
|
B:ASP304
|
3.5
|
32.4
|
1.0
|
|
CG
|
B:ASP311
|
3.6
|
27.2
|
1.0
|
|
C
|
B:ILE313
|
3.6
|
25.7
|
1.0
|
|
C
|
B:LEU309
|
3.6
|
29.8
|
1.0
|
|
CA
|
B:ASP304
|
4.0
|
25.3
|
1.0
|
|
N
|
B:ASP311
|
4.0
|
30.7
|
1.0
|
|
OD2
|
B:ASP311
|
4.1
|
25.1
|
1.0
|
|
N
|
B:ILE313
|
4.2
|
23.9
|
1.0
|
|
CB
|
B:ASP304
|
4.3
|
30.8
|
1.0
|
|
CA
|
B:ILE313
|
4.4
|
23.3
|
1.0
|
|
OD2
|
B:ASP304
|
4.4
|
33.7
|
1.0
|
|
N
|
B:ALA305
|
4.5
|
25.7
|
1.0
|
|
CA
|
B:ALA310
|
4.5
|
33.4
|
1.0
|
|
N
|
B:ALA310
|
4.5
|
31.3
|
1.0
|
|
O
|
B:HOH839
|
4.5
|
46.4
|
1.0
|
|
CA
|
B:LEU309
|
4.6
|
31.1
|
1.0
|
|
N
|
B:VAL314
|
4.6
|
27.6
|
1.0
|
|
CB
|
B:ASP307
|
4.6
|
26.8
|
1.0
|
|
N
|
B:LEU309
|
4.6
|
30.9
|
1.0
|
|
O
|
B:HOH876
|
4.6
|
16.2
|
1.0
|
|
N
|
B:ASP315
|
4.6
|
22.8
|
1.0
|
|
C
|
B:ALA310
|
4.6
|
33.1
|
1.0
|
|
CB
|
B:ASP311
|
4.7
|
25.9
|
1.0
|
|
CA
|
B:VAL314
|
4.7
|
25.8
|
1.0
|
|
CB
|
B:LEU309
|
4.7
|
32.9
|
1.0
|
|
OD2
|
B:ASP315
|
4.8
|
44.6
|
1.0
|
|
CA
|
B:ASP311
|
4.8
|
27.8
|
1.0
|
|
CA
|
B:ALA305
|
4.8
|
26.3
|
1.0
|
|
CB
|
B:ILE313
|
4.8
|
25.7
|
1.0
|
|
N
|
B:GLY312
|
4.9
|
30.6
|
1.0
|
|
Calcium binding site 3 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 3 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 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 Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca701
b:32.9
occ:1.00
|
O
|
C:ILE313
|
2.3
|
31.3
|
1.0
|
|
OD2
|
C:ASP307
|
2.4
|
39.0
|
1.0
|
|
OD1
|
C:ASP304
|
2.4
|
41.5
|
1.0
|
|
OD1
|
C:ASP311
|
2.4
|
39.5
|
1.0
|
|
O
|
C:ASP304
|
2.5
|
36.7
|
1.0
|
|
O
|
C:LEU309
|
2.5
|
35.3
|
1.0
|
|
OD1
|
C:ASP307
|
2.6
|
40.7
|
1.0
|
|
O
|
C:HOH840
|
2.7
|
36.6
|
1.0
|
|
CG
|
C:ASP307
|
2.8
|
39.5
|
1.0
|
|
C
|
C:ASP304
|
3.4
|
36.9
|
1.0
|
|
C
|
C:ILE313
|
3.5
|
30.6
|
1.0
|
|
CG
|
C:ASP311
|
3.5
|
38.3
|
1.0
|
|
CG
|
C:ASP304
|
3.6
|
39.6
|
1.0
|
|
C
|
C:LEU309
|
3.8
|
39.4
|
1.0
|
|
OD2
|
C:ASP311
|
4.0
|
33.5
|
1.0
|
|
CA
|
C:ASP304
|
4.0
|
36.8
|
1.0
|
|
N
|
C:ILE313
|
4.0
|
31.5
|
1.0
|
|
N
|
C:ASP311
|
4.1
|
41.9
|
1.0
|
|
CA
|
C:ILE313
|
4.2
|
30.6
|
1.0
|
|
CB
|
C:ASP307
|
4.3
|
39.2
|
1.0
|
|
N
|
C:ALA305
|
4.4
|
38.1
|
1.0
|
|
CB
|
C:ASP304
|
4.5
|
38.0
|
1.0
|
|
OD2
|
C:ASP315
|
4.5
|
44.5
|
1.0
|
|
N
|
C:VAL314
|
4.5
|
35.3
|
1.0
|
|
CB
|
C:ILE313
|
4.5
|
30.6
|
1.0
|
|
OD2
|
C:ASP304
|
4.5
|
40.7
|
1.0
|
|
N
|
C:ASP315
|
4.6
|
36.7
|
1.0
|
|
CB
|
C:ASP311
|
4.6
|
39.4
|
1.0
|
|
CA
|
C:LEU309
|
4.6
|
40.9
|
1.0
|
|
N
|
C:LEU309
|
4.7
|
40.6
|
1.0
|
|
CA
|
C:ALA305
|
4.7
|
40.4
|
1.0
|
|
N
|
C:ALA310
|
4.7
|
41.5
|
1.0
|
|
CA
|
C:ALA310
|
4.7
|
40.3
|
1.0
|
|
O
|
C:HOH1008
|
4.7
|
22.6
|
1.0
|
|
CA
|
C:VAL314
|
4.7
|
35.1
|
1.0
|
|
CA
|
C:ASP311
|
4.8
|
40.2
|
1.0
|
|
CB
|
C:LEU309
|
4.8
|
42.3
|
1.0
|
|
C
|
C:ALA310
|
4.8
|
42.7
|
1.0
|
|
N
|
C:GLY312
|
4.9
|
35.0
|
1.0
|
|
Calcium binding site 4 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 4 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 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 Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca702
b:21.4
occ:1.00
|
O
|
D:HOH969
|
2.3
|
21.4
|
1.0
|
|
O
|
D:ILE313
|
2.3
|
26.1
|
1.0
|
|
O
|
D:ASP304
|
2.4
|
29.8
|
1.0
|
|
OD1
|
D:ASP304
|
2.4
|
27.6
|
1.0
|
|
OD1
|
D:ASP311
|
2.4
|
29.1
|
1.0
|
|
O
|
D:LEU309
|
2.4
|
34.6
|
1.0
|
|
OD1
|
D:ASP307
|
2.8
|
35.5
|
1.0
|
|
OD2
|
D:ASP307
|
2.8
|
34.3
|
1.0
|
|
CG
|
D:ASP307
|
3.2
|
35.1
|
1.0
|
|
C
|
D:ASP304
|
3.4
|
28.9
|
1.0
|
|
CG
|
D:ASP311
|
3.5
|
28.6
|
1.0
|
|
C
|
D:ILE313
|
3.5
|
24.5
|
1.0
|
|
CG
|
D:ASP304
|
3.6
|
28.9
|
1.0
|
|
C
|
D:LEU309
|
3.7
|
31.8
|
1.0
|
|
CA
|
D:ASP304
|
4.0
|
28.4
|
1.0
|
|
OD2
|
D:ASP311
|
4.0
|
28.9
|
1.0
|
|
N
|
D:ASP311
|
4.0
|
28.5
|
1.0
|
|
N
|
D:ILE313
|
4.2
|
23.7
|
1.0
|
|
CA
|
D:ILE313
|
4.3
|
25.6
|
1.0
|
|
CB
|
D:ASP304
|
4.4
|
27.5
|
1.0
|
|
O
|
D:HOH871
|
4.4
|
30.2
|
1.0
|
|
N
|
D:ALA305
|
4.5
|
29.0
|
1.0
|
|
N
|
D:VAL314
|
4.5
|
27.6
|
1.0
|
|
OD2
|
D:ASP315
|
4.5
|
46.7
|
1.0
|
|
OD2
|
D:ASP304
|
4.6
|
31.5
|
1.0
|
|
N
|
D:ALA310
|
4.6
|
30.0
|
1.0
|
|
CB
|
D:ASP311
|
4.6
|
28.1
|
1.0
|
|
CA
|
D:ALA310
|
4.6
|
28.2
|
1.0
|
|
CA
|
D:LEU309
|
4.6
|
30.1
|
1.0
|
|
CB
|
D:ILE313
|
4.6
|
22.2
|
1.0
|
|
N
|
D:LEU309
|
4.7
|
30.3
|
1.0
|
|
N
|
D:ASP315
|
4.7
|
26.3
|
1.0
|
|
CB
|
D:ASP307
|
4.7
|
30.5
|
1.0
|
|
CA
|
D:VAL314
|
4.7
|
26.8
|
1.0
|
|
CB
|
D:LEU309
|
4.7
|
29.7
|
1.0
|
|
CA
|
D:ASP311
|
4.8
|
25.4
|
1.0
|
|
C
|
D:ALA310
|
4.8
|
30.6
|
1.0
|
|
CA
|
D:ALA305
|
4.8
|
30.7
|
1.0
|
|
N
|
D:GLY312
|
4.9
|
22.4
|
1.0
|
|
Calcium binding site 5 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 5 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 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 Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca701
b:31.6
occ:1.00
|
O
|
E:LEU309
|
2.2
|
37.0
|
1.0
|
|
O
|
E:HOH842
|
2.4
|
30.8
|
1.0
|
|
OD1
|
E:ASP304
|
2.4
|
37.9
|
1.0
|
|
O
|
E:ILE313
|
2.5
|
29.1
|
1.0
|
|
OD2
|
E:ASP307
|
2.5
|
27.9
|
1.0
|
|
OD1
|
E:ASP311
|
2.5
|
40.1
|
1.0
|
|
O
|
E:ASP304
|
2.5
|
49.5
|
1.0
|
|
OD1
|
E:ASP307
|
2.7
|
35.4
|
1.0
|
|
CG
|
E:ASP307
|
3.0
|
37.6
|
1.0
|
|
CG
|
E:ASP311
|
3.4
|
37.9
|
1.0
|
|
C
|
E:LEU309
|
3.5
|
35.4
|
1.0
|
|
C
|
E:ASP304
|
3.5
|
49.6
|
1.0
|
|
CG
|
E:ASP304
|
3.6
|
42.7
|
1.0
|
|
C
|
E:ILE313
|
3.7
|
30.2
|
1.0
|
|
OD2
|
E:ASP311
|
3.7
|
35.4
|
1.0
|
|
CA
|
E:ASP304
|
4.1
|
46.9
|
1.0
|
|
N
|
E:ASP311
|
4.1
|
36.4
|
1.0
|
|
N
|
E:ILE313
|
4.3
|
33.7
|
1.0
|
|
OD2
|
E:ASP315
|
4.4
|
41.8
|
1.0
|
|
CA
|
E:LEU309
|
4.4
|
35.8
|
1.0
|
|
N
|
E:ALA310
|
4.4
|
37.3
|
1.0
|
|
CA
|
E:ALA310
|
4.4
|
37.5
|
1.0
|
|
CA
|
E:ILE313
|
4.4
|
29.9
|
1.0
|
|
CB
|
E:ASP304
|
4.5
|
43.8
|
1.0
|
|
CB
|
E:LEU309
|
4.5
|
35.2
|
1.0
|
|
CB
|
E:ASP307
|
4.5
|
38.7
|
1.0
|
|
N
|
E:ALA305
|
4.5
|
58.5
|
1.0
|
|
N
|
E:LEU309
|
4.5
|
38.8
|
1.0
|
|
OD2
|
E:ASP304
|
4.5
|
43.4
|
1.0
|
|
CB
|
E:ASP311
|
4.6
|
36.8
|
1.0
|
|
CB
|
E:ILE313
|
4.6
|
30.7
|
1.0
|
|
O
|
E:HOH943
|
4.7
|
37.8
|
1.0
|
|
N
|
E:ASP315
|
4.7
|
31.7
|
1.0
|
|
N
|
E:VAL314
|
4.7
|
28.6
|
1.0
|
|
C
|
E:ALA310
|
4.7
|
37.5
|
1.0
|
|
CA
|
E:ALA305
|
4.8
|
59.0
|
1.0
|
|
CA
|
E:ASP311
|
4.9
|
38.2
|
1.0
|
|
CA
|
E:VAL314
|
4.9
|
30.0
|
1.0
|
|
CG
|
E:LEU309
|
4.9
|
35.5
|
1.0
|
|
Calcium binding site 6 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 6 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 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 Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca702
b:36.0
occ:1.00
|
OD1
|
F:ASP311
|
2.3
|
40.0
|
1.0
|
|
O
|
F:LEU309
|
2.4
|
38.0
|
1.0
|
|
O
|
F:ILE313
|
2.4
|
34.8
|
1.0
|
|
OD1
|
F:ASP304
|
2.4
|
36.5
|
1.0
|
|
O
|
F:ASP304
|
2.6
|
43.4
|
1.0
|
|
O
|
F:HOH824
|
2.6
|
37.8
|
1.0
|
|
OD2
|
F:ASP307
|
2.6
|
45.9
|
1.0
|
|
OD1
|
F:ASP307
|
2.7
|
45.7
|
1.0
|
|
CG
|
F:ASP307
|
3.1
|
44.5
|
1.0
|
|
CG
|
F:ASP311
|
3.3
|
41.2
|
1.0
|
|
C
|
F:ASP304
|
3.5
|
39.6
|
1.0
|
|
C
|
F:ILE313
|
3.6
|
33.2
|
1.0
|
|
C
|
F:LEU309
|
3.6
|
39.7
|
1.0
|
|
CG
|
F:ASP304
|
3.6
|
35.5
|
1.0
|
|
OD2
|
F:ASP311
|
3.6
|
41.5
|
1.0
|
|
N
|
F:ASP311
|
4.0
|
43.4
|
1.0
|
|
N
|
F:ILE313
|
4.1
|
35.4
|
1.0
|
|
CA
|
F:ASP304
|
4.1
|
35.9
|
1.0
|
|
CA
|
F:ILE313
|
4.3
|
33.6
|
1.0
|
|
N
|
F:LEU309
|
4.4
|
39.5
|
1.0
|
|
CA
|
F:LEU309
|
4.4
|
40.1
|
1.0
|
|
OD2
|
F:ASP304
|
4.5
|
34.6
|
1.0
|
|
OD2
|
F:ASP315
|
4.5
|
44.6
|
1.0
|
|
N
|
F:ALA310
|
4.5
|
44.0
|
1.0
|
|
CB
|
F:ASP311
|
4.5
|
43.3
|
1.0
|
|
CA
|
F:ALA310
|
4.5
|
44.2
|
1.0
|
|
CB
|
F:ASP304
|
4.5
|
34.7
|
1.0
|
|
CB
|
F:ASP307
|
4.6
|
39.8
|
1.0
|
|
N
|
F:ALA305
|
4.6
|
41.1
|
1.0
|
|
N
|
F:VAL314
|
4.6
|
32.0
|
1.0
|
|
N
|
F:ASP315
|
4.6
|
30.8
|
1.0
|
|
CB
|
F:ILE313
|
4.6
|
33.4
|
1.0
|
|
CB
|
F:LEU309
|
4.7
|
40.4
|
1.0
|
|
C
|
F:ALA310
|
4.7
|
46.8
|
1.0
|
|
O
|
F:HOH1014
|
4.7
|
22.8
|
1.0
|
|
CA
|
F:ASP311
|
4.7
|
43.5
|
1.0
|
|
CA
|
F:VAL314
|
4.8
|
30.2
|
1.0
|
|
CA
|
F:ALA305
|
4.8
|
41.4
|
1.0
|
|
CG2
|
F:ILE313
|
5.0
|
33.2
|
1.0
|
|
N
|
F:GLY312
|
5.0
|
39.3
|
1.0
|
|
Calcium binding site 7 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 7 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 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 Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca701
b:50.6
occ:1.00
|
OD1
|
G:ASP307
|
2.3
|
60.0
|
1.0
|
|
O
|
G:ILE313
|
2.4
|
46.0
|
1.0
|
|
O
|
G:LEU309
|
2.4
|
48.5
|
1.0
|
|
O
|
G:ASP304
|
2.4
|
53.3
|
1.0
|
|
OD1
|
G:ASP311
|
2.5
|
45.9
|
1.0
|
|
OD2
|
G:ASP307
|
2.5
|
60.8
|
1.0
|
|
OD1
|
G:ASP304
|
2.7
|
53.9
|
1.0
|
|
CG
|
G:ASP307
|
2.7
|
60.6
|
1.0
|
|
O
|
G:HOH813
|
2.8
|
44.8
|
1.0
|
|
CG
|
G:ASP311
|
3.4
|
45.9
|
1.0
|
|
C
|
G:ASP304
|
3.5
|
53.1
|
1.0
|
|
C
|
G:LEU309
|
3.6
|
52.1
|
1.0
|
|
C
|
G:ILE313
|
3.6
|
43.4
|
1.0
|
|
CG
|
G:ASP304
|
3.8
|
53.3
|
1.0
|
|
OD2
|
G:ASP311
|
3.8
|
45.8
|
1.0
|
|
N
|
G:ASP311
|
4.0
|
47.8
|
1.0
|
|
CA
|
G:ASP304
|
4.1
|
53.1
|
1.0
|
|
N
|
G:ILE313
|
4.2
|
41.1
|
1.0
|
|
CB
|
G:ASP307
|
4.3
|
59.4
|
1.0
|
|
OD2
|
G:ASP315
|
4.3
|
59.2
|
1.0
|
|
CA
|
G:ILE313
|
4.4
|
42.2
|
1.0
|
|
CA
|
G:LEU309
|
4.4
|
55.0
|
1.0
|
|
N
|
G:LEU309
|
4.4
|
55.6
|
1.0
|
|
N
|
G:ALA305
|
4.5
|
55.0
|
1.0
|
|
N
|
G:ALA310
|
4.5
|
52.9
|
1.0
|
|
N
|
G:VAL314
|
4.5
|
43.8
|
1.0
|
|
CB
|
G:LEU309
|
4.6
|
54.8
|
1.0
|
|
CB
|
G:ASP304
|
4.6
|
52.5
|
1.0
|
|
N
|
G:ASP315
|
4.6
|
48.5
|
1.0
|
|
CA
|
G:ALA310
|
4.6
|
49.9
|
1.0
|
|
CB
|
G:ASP311
|
4.6
|
47.9
|
1.0
|
|
CA
|
G:VAL314
|
4.7
|
45.9
|
1.0
|
|
CB
|
G:ILE313
|
4.7
|
41.2
|
1.0
|
|
OD2
|
G:ASP304
|
4.7
|
53.9
|
1.0
|
|
O
|
G:HOH924
|
4.7
|
46.6
|
1.0
|
|
CA
|
G:ALA305
|
4.8
|
55.5
|
1.0
|
|
CA
|
G:ASP311
|
4.8
|
46.7
|
1.0
|
|
C
|
G:ALA310
|
4.9
|
49.7
|
1.0
|
|
N
|
G:GLY312
|
4.9
|
42.0
|
1.0
|
|
N
|
G:ASP307
|
4.9
|
55.8
|
1.0
|
|
Calcium binding site 8 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 8 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca701
b:48.2
occ:1.00
|
OD1
|
H:ASP304
|
2.3
|
52.3
|
1.0
|
|
O
|
H:LEU309
|
2.3
|
59.0
|
1.0
|
|
OD1
|
H:ASP311
|
2.4
|
46.8
|
1.0
|
|
O
|
H:ILE313
|
2.5
|
48.0
|
1.0
|
|
O
|
H:ASP304
|
2.5
|
56.1
|
1.0
|
|
OD1
|
H:ASP307
|
2.6
|
52.8
|
1.0
|
|
O
|
H:HOH866
|
2.7
|
41.7
|
1.0
|
|
OD2
|
H:ASP307
|
2.7
|
49.0
|
1.0
|
|
CG
|
H:ASP307
|
3.0
|
52.0
|
1.0
|
|
CG
|
H:ASP311
|
3.5
|
48.9
|
1.0
|
|
C
|
H:ASP304
|
3.5
|
55.6
|
1.0
|
|
C
|
H:LEU309
|
3.6
|
57.6
|
1.0
|
|
CG
|
H:ASP304
|
3.6
|
51.3
|
1.0
|
|
C
|
H:ILE313
|
3.7
|
45.6
|
1.0
|
|
N
|
H:ASP311
|
4.0
|
50.7
|
1.0
|
|
OD2
|
H:ASP311
|
4.0
|
47.8
|
1.0
|
|
CA
|
H:ASP304
|
4.1
|
52.8
|
1.0
|
|
OD2
|
H:ASP315
|
4.1
|
54.8
|
1.0
|
|
N
|
H:ILE313
|
4.4
|
42.0
|
1.0
|
|
OD2
|
H:ASP304
|
4.4
|
51.6
|
1.0
|
|
CB
|
H:ASP304
|
4.4
|
50.0
|
1.0
|
|
CA
|
H:LEU309
|
4.4
|
57.5
|
1.0
|
|
N
|
H:LEU309
|
4.5
|
58.5
|
1.0
|
|
N
|
H:ALA310
|
4.5
|
56.6
|
1.0
|
|
N
|
H:ALA305
|
4.5
|
60.0
|
1.0
|
|
CA
|
H:ILE313
|
4.5
|
41.2
|
1.0
|
|
CA
|
H:ALA310
|
4.5
|
54.9
|
1.0
|
|
CB
|
H:ASP307
|
4.6
|
54.1
|
1.0
|
|
CB
|
H:ASP311
|
4.6
|
49.3
|
1.0
|
|
O
|
H:HOH873
|
4.6
|
49.3
|
1.0
|
|
N
|
H:ASP315
|
4.7
|
50.1
|
1.0
|
|
CB
|
H:LEU309
|
4.7
|
55.8
|
1.0
|
|
N
|
H:VAL314
|
4.7
|
44.4
|
1.0
|
|
CA
|
H:VAL314
|
4.8
|
46.6
|
1.0
|
|
CA
|
H:ASP311
|
4.8
|
49.5
|
1.0
|
|
C
|
H:ALA310
|
4.8
|
53.7
|
1.0
|
|
CB
|
H:ILE313
|
4.8
|
41.4
|
1.0
|
|
CA
|
H:ALA305
|
4.8
|
61.0
|
1.0
|
|
Calcium binding site 9 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 9 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca701
b:61.9
occ:1.00
|
O
|
I:LEU309
|
2.2
|
76.5
|
1.0
|
|
OD1
|
I:ASP304
|
2.4
|
83.7
|
1.0
|
|
O
|
I:ILE313
|
2.4
|
62.0
|
1.0
|
|
OD1
|
I:ASP307
|
2.5
|
84.5
|
1.0
|
|
O
|
I:ASP304
|
2.6
|
78.6
|
1.0
|
|
OD1
|
I:ASP311
|
2.8
|
64.3
|
1.0
|
|
OD2
|
I:ASP307
|
2.9
|
79.1
|
1.0
|
|
CG
|
I:ASP307
|
3.1
|
82.4
|
1.0
|
|
C
|
I:LEU309
|
3.5
|
78.2
|
1.0
|
|
CG
|
I:ASP311
|
3.6
|
64.5
|
1.0
|
|
C
|
I:ASP304
|
3.6
|
78.3
|
1.0
|
|
C
|
I:ILE313
|
3.6
|
58.7
|
1.0
|
|
CG
|
I:ASP304
|
3.7
|
82.5
|
1.0
|
|
N
|
I:ASP311
|
3.8
|
63.4
|
1.0
|
|
OD2
|
I:ASP311
|
4.0
|
64.4
|
1.0
|
|
CA
|
I:ASP304
|
4.1
|
75.0
|
1.0
|
|
CA
|
I:ALA310
|
4.2
|
71.0
|
1.0
|
|
N
|
I:ILE313
|
4.2
|
52.8
|
1.0
|
|
N
|
I:ALA310
|
4.3
|
74.9
|
1.0
|
|
CA
|
I:ILE313
|
4.4
|
53.8
|
1.0
|
|
CB
|
I:ASP304
|
4.5
|
80.1
|
1.0
|
|
C
|
I:ALA310
|
4.5
|
66.7
|
1.0
|
|
CA
|
I:LEU309
|
4.5
|
81.3
|
1.0
|
|
OD2
|
I:ASP304
|
4.6
|
82.8
|
1.0
|
|
CB
|
I:ASP307
|
4.6
|
83.3
|
1.0
|
|
OD2
|
I:ASP315
|
4.6
|
72.8
|
1.0
|
|
N
|
I:LEU309
|
4.6
|
83.2
|
1.0
|
|
N
|
I:VAL314
|
4.6
|
63.0
|
1.0
|
|
N
|
I:ALA305
|
4.7
|
77.6
|
1.0
|
|
CB
|
I:ASP311
|
4.7
|
64.1
|
1.0
|
|
N
|
I:ASP315
|
4.7
|
73.0
|
1.0
|
|
CB
|
I:ILE313
|
4.7
|
49.4
|
1.0
|
|
CA
|
I:ASP311
|
4.7
|
62.5
|
1.0
|
|
O
|
I:HOH891
|
4.7
|
44.2
|
1.0
|
|
CB
|
I:LEU309
|
4.8
|
82.3
|
1.0
|
|
CA
|
I:VAL314
|
4.8
|
68.5
|
1.0
|
|
N
|
I:GLY312
|
4.9
|
57.6
|
1.0
|
|
Calcium binding site 10 out
of 10 in 6qg9
Go back to
Calcium Binding Sites List in 6qg9
Calcium binding site 10 out
of 10 in the Crystal Structure of Ideonella Sakaiensis Mhetase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ca701
b:61.3
occ:1.00
|
O
|
J:ILE313
|
2.3
|
52.9
|
1.0
|
|
OD2
|
J:ASP307
|
2.3
|
73.5
|
1.0
|
|
OD1
|
J:ASP304
|
2.4
|
61.7
|
1.0
|
|
O
|
J:LEU309
|
2.5
|
63.1
|
1.0
|
|
OD1
|
J:ASP311
|
2.7
|
60.9
|
1.0
|
|
OD1
|
J:ASP307
|
2.7
|
73.2
|
1.0
|
|
CG
|
J:ASP307
|
2.9
|
73.1
|
1.0
|
|
O
|
J:ASP304
|
3.1
|
64.3
|
1.0
|
|
C
|
J:ILE313
|
3.5
|
51.4
|
1.0
|
|
CG
|
J:ASP311
|
3.6
|
61.0
|
1.0
|
|
CG
|
J:ASP304
|
3.7
|
60.3
|
1.0
|
|
C
|
J:LEU309
|
3.7
|
63.4
|
1.0
|
|
OD2
|
J:ASP315
|
3.9
|
66.7
|
1.0
|
|
N
|
J:ASP311
|
4.0
|
55.7
|
1.0
|
|
C
|
J:ASP304
|
4.0
|
63.3
|
1.0
|
|
OD2
|
J:ASP311
|
4.1
|
60.8
|
1.0
|
|
N
|
J:ILE313
|
4.1
|
44.8
|
1.0
|
|
CA
|
J:ILE313
|
4.2
|
44.9
|
1.0
|
|
CA
|
J:ASP304
|
4.4
|
61.6
|
1.0
|
|
CB
|
J:ASP307
|
4.4
|
71.4
|
1.0
|
|
CB
|
J:ILE313
|
4.4
|
51.4
|
1.0
|
|
OD2
|
J:ASP304
|
4.4
|
58.4
|
1.0
|
|
N
|
J:VAL314
|
4.5
|
53.2
|
1.0
|
|
CA
|
J:ALA310
|
4.5
|
58.2
|
1.0
|
|
N
|
J:ASP315
|
4.5
|
62.6
|
1.0
|
|
N
|
J:ALA310
|
4.5
|
61.1
|
1.0
|
|
CB
|
J:ASP304
|
4.6
|
60.7
|
1.0
|
|
CA
|
J:VAL314
|
4.7
|
56.0
|
1.0
|
|
CA
|
J:LEU309
|
4.7
|
63.0
|
1.0
|
|
CB
|
J:ASP311
|
4.7
|
58.8
|
1.0
|
|
C
|
J:ALA310
|
4.7
|
56.9
|
1.0
|
|
N
|
J:LEU309
|
4.7
|
62.5
|
1.0
|
|
CA
|
J:ASP311
|
4.8
|
55.8
|
1.0
|
|
CG2
|
J:ILE313
|
4.9
|
45.5
|
1.0
|
|
CG
|
J:ASP315
|
4.9
|
66.4
|
1.0
|
|
CB
|
J:LEU309
|
4.9
|
66.4
|
1.0
|
|
N
|
J:GLY312
|
4.9
|
51.1
|
1.0
|
|
Reference:
G.J.Palm,
L.Reisky,
D.Bottcher,
H.Muller,
E.A.P.Michels,
M.C.Walczak,
L.Berndt,
M.S.Weiss,
U.T.Bornscheuer,
G.Weber.
Structure of the Plastic-Degrading Ideonella Sakaiensis Mhetase Bound to A Substrate. Nat Commun V. 10 1717 2019.
ISSN: ESSN 2041-1723
PubMed: 30979881
DOI: 10.1038/S41467-019-09326-3
Page generated: Wed Jul 9 17:10:35 2025
|
