Calcium in PDB 6qga: Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
Enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
All present enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta:
3.1.1.102;
Protein crystallography data
The structure of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta, PDB code: 6qga
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)
|
49.11 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.153,
183.646,
246.752,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.3 /
19.8
|
Other elements in 6qga:
The structure of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
(pdb code 6qga). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta, PDB code: 6qga:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6qga
Go back to
Calcium Binding Sites List in 6qga
Calcium binding site 1 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
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 Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca706
b:25.8
occ:1.00
|
OD1
|
A:ASP304
|
2.3
|
32.1
|
1.0
|
O
|
A:ILE313
|
2.4
|
29.9
|
1.0
|
O
|
A:LEU309
|
2.4
|
32.2
|
1.0
|
OD1
|
A:ASP311
|
2.6
|
30.6
|
1.0
|
OD2
|
A:ASP307
|
2.6
|
29.9
|
1.0
|
O
|
A:HOH822
|
2.6
|
25.8
|
1.0
|
O
|
A:ASP304
|
2.6
|
32.2
|
1.0
|
OD1
|
A:ASP307
|
2.7
|
30.9
|
1.0
|
CG
|
A:ASP307
|
3.0
|
30.3
|
1.0
|
C
|
A:ASP304
|
3.4
|
33.1
|
1.0
|
CG
|
A:ASP304
|
3.5
|
33.0
|
1.0
|
CG
|
A:ASP311
|
3.5
|
30.4
|
1.0
|
C
|
A:ILE313
|
3.6
|
29.4
|
1.0
|
C
|
A:LEU309
|
3.6
|
32.9
|
1.0
|
OD2
|
A:ASP311
|
3.9
|
29.7
|
1.0
|
CA
|
A:ASP304
|
3.9
|
33.1
|
1.0
|
N
|
A:ASP311
|
4.0
|
32.6
|
1.0
|
N
|
A:ILE313
|
4.2
|
30.2
|
1.0
|
CB
|
A:ASP304
|
4.3
|
33.6
|
1.0
|
OD2
|
A:ASP315
|
4.4
|
36.4
|
1.0
|
CA
|
A:ILE313
|
4.4
|
29.3
|
1.0
|
OD2
|
A:ASP304
|
4.4
|
33.4
|
1.0
|
N
|
A:ALA305
|
4.5
|
34.2
|
1.0
|
CA
|
A:LEU309
|
4.5
|
32.8
|
1.0
|
CB
|
A:ASP307
|
4.5
|
30.1
|
1.0
|
N
|
A:ALA310
|
4.5
|
33.8
|
1.0
|
O
|
A:HOH936
|
4.5
|
24.8
|
1.0
|
N
|
A:LEU309
|
4.5
|
32.7
|
1.0
|
N
|
A:VAL314
|
4.6
|
29.2
|
1.0
|
CA
|
A:ALA310
|
4.6
|
34.1
|
1.0
|
N
|
A:ASP315
|
4.7
|
28.4
|
1.0
|
CB
|
A:LEU309
|
4.7
|
31.8
|
1.0
|
CB
|
A:ASP311
|
4.7
|
31.1
|
1.0
|
CA
|
A:VAL314
|
4.7
|
29.4
|
1.0
|
CB
|
A:ILE313
|
4.7
|
28.5
|
1.0
|
C
|
A:ALA310
|
4.8
|
33.5
|
1.0
|
CA
|
A:ALA305
|
4.8
|
34.4
|
1.0
|
CA
|
A:ASP311
|
4.8
|
32.0
|
1.0
|
N
|
A:GLY312
|
4.9
|
32.0
|
1.0
|
O
|
A:HOH1055
|
4.9
|
25.8
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6qga
Go back to
Calcium Binding Sites List in 6qga
Calcium binding site 2 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
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 Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca706
b:23.9
occ:1.00
|
O
|
B:LEU309
|
2.3
|
28.8
|
1.0
|
O
|
B:ILE313
|
2.4
|
25.9
|
1.0
|
OD1
|
B:ASP304
|
2.5
|
27.9
|
1.0
|
O
|
B:ASP304
|
2.5
|
27.6
|
1.0
|
OD1
|
B:ASP311
|
2.5
|
27.4
|
1.0
|
O
|
B:HOH870
|
2.6
|
25.6
|
1.0
|
OD1
|
B:ASP307
|
2.6
|
27.5
|
1.0
|
OD2
|
B:ASP307
|
2.7
|
26.1
|
1.0
|
CG
|
B:ASP307
|
3.0
|
26.7
|
1.0
|
C
|
B:ASP304
|
3.5
|
28.0
|
1.0
|
CG
|
B:ASP311
|
3.5
|
27.7
|
1.0
|
C
|
B:LEU309
|
3.5
|
29.6
|
1.0
|
C
|
B:ILE313
|
3.6
|
25.4
|
1.0
|
CG
|
B:ASP304
|
3.7
|
28.3
|
1.0
|
OD2
|
B:ASP311
|
4.0
|
28.5
|
1.0
|
N
|
B:ASP311
|
4.0
|
29.3
|
1.0
|
CA
|
B:ASP304
|
4.1
|
27.6
|
1.0
|
N
|
B:ILE313
|
4.2
|
26.4
|
1.0
|
CA
|
B:LEU309
|
4.4
|
29.8
|
1.0
|
CA
|
B:ILE313
|
4.4
|
25.5
|
1.0
|
N
|
B:ALA310
|
4.4
|
30.4
|
1.0
|
CB
|
B:ASP304
|
4.5
|
28.3
|
1.0
|
N
|
B:LEU309
|
4.5
|
29.6
|
1.0
|
N
|
B:ALA305
|
4.5
|
28.8
|
1.0
|
CB
|
B:LEU309
|
4.5
|
29.3
|
1.0
|
O
|
B:HOH865
|
4.5
|
20.6
|
1.0
|
CA
|
B:ALA310
|
4.5
|
30.4
|
1.0
|
CB
|
B:ASP307
|
4.5
|
26.5
|
1.0
|
OD2
|
B:ASP304
|
4.6
|
28.8
|
1.0
|
CB
|
B:ASP311
|
4.6
|
28.6
|
1.0
|
N
|
B:VAL314
|
4.6
|
24.8
|
1.0
|
OD2
|
B:ASP315
|
4.7
|
33.9
|
1.0
|
CB
|
B:ILE313
|
4.7
|
25.3
|
1.0
|
C
|
B:ALA310
|
4.7
|
30.2
|
1.0
|
N
|
B:ASP315
|
4.7
|
24.4
|
1.0
|
CA
|
B:ALA305
|
4.7
|
29.4
|
1.0
|
CA
|
B:ASP311
|
4.8
|
29.1
|
1.0
|
CA
|
B:VAL314
|
4.8
|
24.7
|
1.0
|
N
|
B:GLY312
|
5.0
|
28.2
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6qga
Go back to
Calcium Binding Sites List in 6qga
Calcium binding site 3 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
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 Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca703
b:30.9
occ:1.00
|
O
|
C:ASP304
|
2.4
|
34.6
|
1.0
|
OD1
|
C:ASP304
|
2.4
|
35.5
|
1.0
|
O
|
C:ILE313
|
2.4
|
32.2
|
1.0
|
O
|
C:LEU309
|
2.4
|
36.2
|
1.0
|
OD1
|
C:ASP311
|
2.4
|
34.1
|
1.0
|
OD1
|
C:ASP307
|
2.5
|
34.2
|
1.0
|
O
|
C:HOH826
|
2.5
|
27.2
|
1.0
|
OD2
|
C:ASP307
|
2.6
|
32.5
|
1.0
|
CG
|
C:ASP307
|
2.9
|
33.2
|
1.0
|
C
|
C:ASP304
|
3.4
|
35.3
|
1.0
|
CG
|
C:ASP311
|
3.5
|
34.3
|
1.0
|
C
|
C:ILE313
|
3.6
|
31.5
|
1.0
|
CG
|
C:ASP304
|
3.6
|
35.5
|
1.0
|
C
|
C:LEU309
|
3.6
|
37.3
|
1.0
|
N
|
C:ASP311
|
4.0
|
36.6
|
1.0
|
CA
|
C:ASP304
|
4.0
|
34.8
|
1.0
|
OD2
|
C:ASP311
|
4.0
|
34.8
|
1.0
|
N
|
C:ILE313
|
4.2
|
32.7
|
1.0
|
OD2
|
C:ASP315
|
4.3
|
35.8
|
1.0
|
N
|
C:ALA305
|
4.4
|
36.5
|
1.0
|
CA
|
C:ILE313
|
4.4
|
31.5
|
1.0
|
CB
|
C:ASP307
|
4.4
|
33.0
|
1.0
|
CB
|
C:ASP304
|
4.4
|
35.6
|
1.0
|
O
|
C:HOH824
|
4.4
|
26.5
|
1.0
|
CA
|
C:LEU309
|
4.5
|
37.5
|
1.0
|
OD2
|
C:ASP304
|
4.5
|
36.0
|
1.0
|
N
|
C:LEU309
|
4.5
|
37.3
|
1.0
|
N
|
C:ALA310
|
4.6
|
38.4
|
1.0
|
CB
|
C:LEU309
|
4.6
|
36.7
|
1.0
|
CA
|
C:ALA310
|
4.6
|
38.3
|
1.0
|
CB
|
C:ASP311
|
4.6
|
35.6
|
1.0
|
N
|
C:VAL314
|
4.6
|
30.7
|
1.0
|
N
|
C:ASP315
|
4.6
|
30.2
|
1.0
|
CA
|
C:ALA305
|
4.7
|
37.3
|
1.0
|
CB
|
C:ILE313
|
4.7
|
31.0
|
1.0
|
C
|
C:ALA310
|
4.7
|
37.9
|
1.0
|
CA
|
C:VAL314
|
4.8
|
30.7
|
1.0
|
CA
|
C:ASP311
|
4.8
|
36.2
|
1.0
|
N
|
C:GLY312
|
5.0
|
35.2
|
1.0
|
N
|
C:ASP307
|
5.0
|
34.5
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6qga
Go back to
Calcium Binding Sites List in 6qga
Calcium binding site 4 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
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 Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca702
b:21.9
occ:1.00
|
O
|
D:LEU309
|
2.3
|
25.0
|
1.0
|
O
|
D:ILE313
|
2.4
|
23.8
|
1.0
|
OD1
|
D:ASP304
|
2.4
|
25.9
|
1.0
|
O
|
D:HOH824
|
2.5
|
24.4
|
1.0
|
OD2
|
D:ASP307
|
2.6
|
26.4
|
1.0
|
O
|
D:ASP304
|
2.6
|
24.8
|
1.0
|
OD1
|
D:ASP311
|
2.7
|
24.5
|
1.0
|
OD1
|
D:ASP307
|
2.7
|
24.9
|
1.0
|
CG
|
D:ASP307
|
3.0
|
25.9
|
1.0
|
C
|
D:ASP304
|
3.5
|
25.3
|
1.0
|
C
|
D:LEU309
|
3.5
|
25.5
|
1.0
|
C
|
D:ILE313
|
3.6
|
23.7
|
1.0
|
CG
|
D:ASP304
|
3.6
|
25.7
|
1.0
|
CG
|
D:ASP311
|
3.6
|
26.2
|
1.0
|
OD2
|
D:ASP311
|
4.0
|
27.3
|
1.0
|
CA
|
D:ASP304
|
4.0
|
25.4
|
1.0
|
N
|
D:ASP311
|
4.0
|
25.8
|
1.0
|
N
|
D:ILE313
|
4.2
|
24.5
|
1.0
|
CA
|
D:ILE313
|
4.3
|
23.8
|
1.0
|
CB
|
D:ASP304
|
4.4
|
25.9
|
1.0
|
OD2
|
D:ASP315
|
4.4
|
29.4
|
1.0
|
CA
|
D:LEU309
|
4.4
|
25.3
|
1.0
|
N
|
D:ALA310
|
4.4
|
26.1
|
1.0
|
N
|
D:LEU309
|
4.5
|
25.1
|
1.0
|
OD2
|
D:ASP304
|
4.5
|
26.2
|
1.0
|
CA
|
D:ALA310
|
4.5
|
26.4
|
1.0
|
CB
|
D:ASP307
|
4.5
|
23.4
|
1.0
|
N
|
D:VAL314
|
4.6
|
23.4
|
1.0
|
N
|
D:ALA305
|
4.6
|
28.9
|
1.0
|
CB
|
D:LEU309
|
4.6
|
24.9
|
1.0
|
O
|
D:HOH963
|
4.6
|
21.4
|
1.0
|
N
|
D:ASP315
|
4.7
|
22.6
|
1.0
|
CB
|
D:ILE313
|
4.7
|
23.4
|
1.0
|
CB
|
D:ASP311
|
4.7
|
25.5
|
1.0
|
C
|
D:ALA310
|
4.8
|
26.4
|
1.0
|
CA
|
D:VAL314
|
4.8
|
23.4
|
1.0
|
CA
|
D:ASP311
|
4.8
|
25.8
|
1.0
|
CA
|
D:ALA305
|
4.9
|
26.2
|
1.0
|
N
|
D:GLY312
|
5.0
|
25.8
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6qga
Go back to
Calcium Binding Sites List in 6qga
Calcium binding site 5 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
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 Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca705
b:26.2
occ:1.00
|
OD1
|
E:ASP304
|
2.3
|
30.2
|
1.0
|
O
|
E:ILE313
|
2.3
|
24.3
|
1.0
|
OD1
|
E:ASP311
|
2.4
|
25.2
|
1.0
|
O
|
E:LEU309
|
2.4
|
26.4
|
1.0
|
OD2
|
E:ASP307
|
2.5
|
27.6
|
1.0
|
O
|
E:HOH812
|
2.6
|
26.1
|
1.0
|
OD1
|
E:ASP307
|
2.6
|
27.8
|
1.0
|
O
|
E:ASP304
|
2.7
|
25.8
|
1.0
|
CG
|
E:ASP307
|
2.9
|
26.1
|
1.0
|
CG
|
E:ASP311
|
3.4
|
25.4
|
1.0
|
C
|
E:ILE313
|
3.5
|
23.9
|
1.0
|
C
|
E:ASP304
|
3.5
|
29.9
|
1.0
|
CG
|
E:ASP304
|
3.6
|
28.9
|
1.0
|
C
|
E:LEU309
|
3.6
|
27.0
|
1.0
|
OD2
|
E:ASP311
|
3.8
|
25.4
|
1.0
|
N
|
E:ASP311
|
4.0
|
26.4
|
1.0
|
CA
|
E:ASP304
|
4.0
|
25.7
|
1.0
|
N
|
E:ILE313
|
4.1
|
24.4
|
1.0
|
CA
|
E:ILE313
|
4.3
|
23.9
|
1.0
|
OD2
|
E:ASP315
|
4.3
|
30.9
|
1.0
|
CB
|
E:ASP304
|
4.4
|
26.0
|
1.0
|
OD2
|
E:ASP304
|
4.4
|
26.2
|
1.0
|
CB
|
E:ASP307
|
4.5
|
25.2
|
1.0
|
CA
|
E:LEU309
|
4.5
|
27.2
|
1.0
|
O
|
E:HOH940
|
4.5
|
19.6
|
1.0
|
N
|
E:ALA310
|
4.5
|
27.5
|
1.0
|
N
|
E:VAL314
|
4.6
|
23.6
|
1.0
|
CA
|
E:ALA310
|
4.6
|
27.3
|
1.0
|
CB
|
E:ASP311
|
4.6
|
26.0
|
1.0
|
N
|
E:ALA305
|
4.6
|
26.7
|
1.0
|
CB
|
E:ILE313
|
4.6
|
23.7
|
1.0
|
N
|
E:LEU309
|
4.6
|
27.1
|
1.0
|
CB
|
E:LEU309
|
4.6
|
26.9
|
1.0
|
N
|
E:ASP315
|
4.7
|
24.0
|
1.0
|
CA
|
E:ASP311
|
4.7
|
26.2
|
1.0
|
CA
|
E:VAL314
|
4.7
|
23.6
|
1.0
|
C
|
E:ALA310
|
4.8
|
27.1
|
1.0
|
N
|
E:GLY312
|
4.9
|
25.6
|
1.0
|
CA
|
E:ALA305
|
4.9
|
27.1
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6qga
Go back to
Calcium Binding Sites List in 6qga
Calcium binding site 6 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta
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 Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca706
b:24.8
occ:1.00
|
O
|
F:ILE313
|
2.3
|
25.3
|
1.0
|
O
|
F:LEU309
|
2.4
|
27.5
|
1.0
|
OD1
|
F:ASP311
|
2.4
|
26.6
|
1.0
|
OD1
|
F:ASP304
|
2.4
|
26.9
|
1.0
|
O
|
F:HOH860
|
2.5
|
26.8
|
1.0
|
OD2
|
F:ASP307
|
2.5
|
25.4
|
1.0
|
O
|
F:ASP304
|
2.6
|
26.6
|
1.0
|
OD1
|
F:ASP307
|
2.7
|
27.7
|
1.0
|
CG
|
F:ASP307
|
3.0
|
25.8
|
1.0
|
CG
|
F:ASP311
|
3.5
|
26.9
|
1.0
|
C
|
F:ASP304
|
3.5
|
26.9
|
1.0
|
C
|
F:ILE313
|
3.5
|
24.9
|
1.0
|
C
|
F:LEU309
|
3.6
|
28.2
|
1.0
|
CG
|
F:ASP304
|
3.6
|
27.2
|
1.0
|
OD2
|
F:ASP311
|
4.0
|
26.6
|
1.0
|
N
|
F:ASP311
|
4.0
|
28.0
|
1.0
|
CA
|
F:ASP304
|
4.0
|
26.7
|
1.0
|
N
|
F:ILE313
|
4.1
|
25.8
|
1.0
|
CA
|
F:ILE313
|
4.3
|
25.1
|
1.0
|
CB
|
F:ASP304
|
4.4
|
27.2
|
1.0
|
O
|
F:HOH947
|
4.4
|
19.1
|
1.0
|
CA
|
F:LEU309
|
4.5
|
28.4
|
1.0
|
CB
|
F:ASP307
|
4.5
|
25.7
|
1.0
|
N
|
F:ALA310
|
4.5
|
28.9
|
1.0
|
OD2
|
F:ASP315
|
4.5
|
31.9
|
1.0
|
CA
|
F:ALA310
|
4.5
|
28.8
|
1.0
|
N
|
F:ALA305
|
4.5
|
27.6
|
1.0
|
OD2
|
F:ASP304
|
4.5
|
27.6
|
1.0
|
N
|
F:LEU309
|
4.5
|
28.1
|
1.0
|
N
|
F:VAL314
|
4.6
|
24.4
|
1.0
|
CB
|
F:LEU309
|
4.6
|
28.1
|
1.0
|
CB
|
F:ILE313
|
4.6
|
24.9
|
1.0
|
CB
|
F:ASP311
|
4.6
|
27.7
|
1.0
|
N
|
F:ASP315
|
4.7
|
24.1
|
1.0
|
C
|
F:ALA310
|
4.7
|
28.7
|
1.0
|
CA
|
F:ASP311
|
4.7
|
28.0
|
1.0
|
CA
|
F:VAL314
|
4.8
|
24.3
|
1.0
|
CA
|
F:ALA305
|
4.8
|
28.0
|
1.0
|
N
|
F:GLY312
|
4.9
|
27.3
|
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: Tue Jul 16 13:49:15 2024
|