Calcium in PDB 6qgb: Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid
Enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid
All present enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid:
3.1.1.102;
Protein crystallography data
The structure of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid, PDB code: 6qgb
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)
|
46.09 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.141,
184.048,
247.441,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
21.4
|
Other elements in 6qgb:
The structure of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid 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 Benzoic Acid
(pdb code 6qgb). 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 Benzoic Acid, PDB code: 6qgb:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6qgb
Go back to
Calcium Binding Sites List in 6qgb
Calcium binding site 1 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid
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 Benzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:27.4
occ:1.00
|
OD1
|
A:ASP304
|
2.3
|
32.5
|
1.0
|
O
|
A:ILE313
|
2.3
|
30.7
|
1.0
|
O
|
A:LEU309
|
2.4
|
32.6
|
1.0
|
O
|
A:HOH809
|
2.5
|
34.8
|
1.0
|
O
|
A:ASP304
|
2.5
|
32.8
|
1.0
|
OD2
|
A:ASP307
|
2.5
|
36.0
|
1.0
|
OD1
|
A:ASP311
|
2.6
|
31.2
|
1.0
|
OD1
|
A:ASP307
|
2.6
|
31.6
|
1.0
|
CG
|
A:ASP307
|
2.9
|
31.1
|
1.0
|
C
|
A:ASP304
|
3.4
|
33.6
|
1.0
|
CG
|
A:ASP304
|
3.5
|
33.3
|
1.0
|
CG
|
A:ASP311
|
3.5
|
31.1
|
1.0
|
C
|
A:ILE313
|
3.5
|
30.3
|
1.0
|
C
|
A:LEU309
|
3.6
|
33.3
|
1.0
|
OD2
|
A:ASP311
|
3.9
|
30.5
|
1.0
|
CA
|
A:ASP304
|
4.0
|
33.6
|
1.0
|
N
|
A:ASP311
|
4.1
|
33.1
|
1.0
|
N
|
A:ILE313
|
4.1
|
30.9
|
1.0
|
OD2
|
A:ASP315
|
4.2
|
31.1
|
1.0
|
CA
|
A:ILE313
|
4.3
|
30.2
|
1.0
|
CB
|
A:ASP304
|
4.3
|
34.0
|
1.0
|
OD2
|
A:ASP304
|
4.3
|
33.7
|
1.0
|
CB
|
A:ASP307
|
4.4
|
31.0
|
1.0
|
CA
|
A:LEU309
|
4.5
|
33.2
|
1.0
|
N
|
A:ALA305
|
4.5
|
34.7
|
1.0
|
N
|
A:LEU309
|
4.5
|
33.2
|
1.0
|
N
|
A:ALA310
|
4.5
|
34.2
|
1.0
|
N
|
A:VAL314
|
4.5
|
30.2
|
1.0
|
CA
|
A:ALA310
|
4.6
|
34.5
|
1.0
|
O
|
A:HOH957
|
4.6
|
25.8
|
1.0
|
CB
|
A:LEU309
|
4.6
|
32.3
|
1.0
|
CB
|
A:ILE313
|
4.6
|
29.6
|
1.0
|
CB
|
A:ASP311
|
4.7
|
31.8
|
1.0
|
N
|
A:ASP315
|
4.7
|
29.6
|
1.0
|
CA
|
A:VAL314
|
4.7
|
30.4
|
1.0
|
C
|
A:ALA310
|
4.8
|
33.9
|
1.0
|
CA
|
A:ASP311
|
4.8
|
32.6
|
1.0
|
CA
|
A:ALA305
|
4.8
|
35.0
|
1.0
|
N
|
A:GLY312
|
4.8
|
32.5
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6qgb
Go back to
Calcium Binding Sites List in 6qgb
Calcium binding site 2 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid
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 Benzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca803
b:28.9
occ:1.00
|
O
|
B:LEU309
|
2.3
|
33.1
|
1.0
|
O
|
B:HOH967
|
2.4
|
33.2
|
1.0
|
OD1
|
B:ASP304
|
2.4
|
35.7
|
1.0
|
OD1
|
B:ASP311
|
2.4
|
34.1
|
1.0
|
O
|
B:ILE313
|
2.4
|
30.2
|
1.0
|
OD1
|
B:ASP307
|
2.6
|
31.9
|
1.0
|
OD2
|
B:ASP307
|
2.6
|
30.6
|
1.0
|
O
|
B:ASP304
|
2.7
|
34.7
|
1.0
|
CG
|
B:ASP307
|
3.0
|
31.2
|
1.0
|
CG
|
B:ASP311
|
3.4
|
31.9
|
1.0
|
C
|
B:LEU309
|
3.5
|
33.9
|
1.0
|
C
|
B:ASP304
|
3.6
|
32.2
|
1.0
|
CG
|
B:ASP304
|
3.6
|
33.4
|
1.0
|
C
|
B:ILE313
|
3.6
|
29.6
|
1.0
|
OD2
|
B:ASP311
|
3.9
|
31.9
|
1.0
|
N
|
B:ASP311
|
4.0
|
33.3
|
1.0
|
CA
|
B:ASP304
|
4.1
|
31.8
|
1.0
|
N
|
B:ILE313
|
4.2
|
30.5
|
1.0
|
CA
|
B:ILE313
|
4.4
|
29.7
|
1.0
|
CA
|
B:LEU309
|
4.4
|
34.2
|
1.0
|
OD2
|
B:ASP315
|
4.4
|
34.1
|
1.0
|
N
|
B:LEU309
|
4.4
|
34.0
|
1.0
|
CB
|
B:ASP304
|
4.5
|
32.3
|
1.0
|
CB
|
B:LEU309
|
4.5
|
33.9
|
1.0
|
CB
|
B:ASP307
|
4.5
|
31.1
|
1.0
|
OD2
|
B:ASP304
|
4.5
|
33.2
|
1.0
|
N
|
B:ALA310
|
4.5
|
34.6
|
1.0
|
O
|
B:HOH955
|
4.5
|
26.9
|
1.0
|
CA
|
B:ALA310
|
4.6
|
34.5
|
1.0
|
CB
|
B:ASP311
|
4.6
|
32.7
|
1.0
|
CB
|
B:ILE313
|
4.6
|
29.5
|
1.0
|
N
|
B:ALA305
|
4.7
|
37.8
|
1.0
|
N
|
B:VAL314
|
4.7
|
29.0
|
1.0
|
CA
|
B:ASP311
|
4.7
|
33.1
|
1.0
|
C
|
B:ALA310
|
4.7
|
34.2
|
1.0
|
N
|
B:ASP315
|
4.7
|
28.9
|
1.0
|
CA
|
B:VAL314
|
4.8
|
29.0
|
1.0
|
N
|
B:GLY312
|
4.9
|
32.2
|
1.0
|
CA
|
B:ALA305
|
5.0
|
35.0
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6qgb
Go back to
Calcium Binding Sites List in 6qgb
Calcium binding site 3 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid
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 Benzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca702
b:33.7
occ:1.00
|
O
|
C:HOH887
|
2.4
|
31.5
|
1.0
|
O
|
C:LEU309
|
2.4
|
40.4
|
1.0
|
OD1
|
C:ASP304
|
2.4
|
35.8
|
1.0
|
O
|
C:ASP304
|
2.4
|
36.0
|
1.0
|
O
|
C:ILE313
|
2.4
|
33.7
|
1.0
|
OD1
|
C:ASP307
|
2.5
|
43.1
|
1.0
|
OD2
|
C:ASP307
|
2.5
|
40.0
|
1.0
|
OD1
|
C:ASP311
|
2.5
|
37.0
|
1.0
|
CG
|
C:ASP307
|
2.8
|
36.1
|
1.0
|
C
|
C:ASP304
|
3.4
|
36.5
|
1.0
|
C
|
C:LEU309
|
3.6
|
37.7
|
1.0
|
CG
|
C:ASP311
|
3.6
|
36.8
|
1.0
|
CG
|
C:ASP304
|
3.6
|
36.2
|
1.0
|
C
|
C:ILE313
|
3.6
|
33.1
|
1.0
|
CA
|
C:ASP304
|
4.0
|
36.0
|
1.0
|
OD2
|
C:ASP311
|
4.1
|
37.2
|
1.0
|
N
|
C:ASP311
|
4.2
|
36.9
|
1.0
|
O
|
C:HOH815
|
4.3
|
31.4
|
1.0
|
CB
|
C:ASP307
|
4.3
|
34.9
|
1.0
|
N
|
C:ILE313
|
4.3
|
33.9
|
1.0
|
OD2
|
C:ASP315
|
4.3
|
35.1
|
1.0
|
CB
|
C:ASP304
|
4.4
|
36.5
|
1.0
|
N
|
C:ALA305
|
4.4
|
37.4
|
1.0
|
CA
|
C:ILE313
|
4.4
|
33.0
|
1.0
|
CA
|
C:LEU309
|
4.5
|
37.9
|
1.0
|
OD2
|
C:ASP304
|
4.5
|
36.6
|
1.0
|
N
|
C:ALA310
|
4.5
|
38.4
|
1.0
|
CA
|
C:ALA310
|
4.5
|
38.3
|
1.0
|
N
|
C:LEU309
|
4.5
|
38.0
|
1.0
|
N
|
C:ASP315
|
4.6
|
33.3
|
1.0
|
N
|
C:VAL314
|
4.6
|
32.6
|
1.0
|
CB
|
C:LEU309
|
4.7
|
37.3
|
1.0
|
CA
|
C:ALA305
|
4.7
|
38.0
|
1.0
|
CB
|
C:ILE313
|
4.7
|
32.6
|
1.0
|
CA
|
C:VAL314
|
4.7
|
32.7
|
1.0
|
C
|
C:ALA310
|
4.8
|
37.8
|
1.0
|
CB
|
C:ASP311
|
4.8
|
35.9
|
1.0
|
CA
|
C:ASP311
|
4.9
|
36.4
|
1.0
|
N
|
C:ASP307
|
5.0
|
36.1
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6qgb
Go back to
Calcium Binding Sites List in 6qgb
Calcium binding site 4 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid
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 Benzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca702
b:29.1
occ:1.00
|
O
|
D:LEU309
|
2.3
|
28.1
|
1.0
|
O
|
D:ILE313
|
2.4
|
27.2
|
1.0
|
OD1
|
D:ASP304
|
2.4
|
28.4
|
1.0
|
O
|
D:HOH923
|
2.4
|
27.9
|
1.0
|
OD2
|
D:ASP307
|
2.6
|
28.7
|
1.0
|
O
|
D:ASP304
|
2.6
|
28.2
|
1.0
|
OD1
|
D:ASP307
|
2.6
|
28.6
|
1.0
|
OD1
|
D:ASP311
|
2.8
|
32.4
|
1.0
|
CG
|
D:ASP307
|
3.0
|
28.0
|
1.0
|
C
|
D:LEU309
|
3.5
|
28.3
|
1.0
|
C
|
D:ASP304
|
3.5
|
28.6
|
1.0
|
C
|
D:ILE313
|
3.6
|
27.1
|
1.0
|
CG
|
D:ASP304
|
3.6
|
28.7
|
1.0
|
CG
|
D:ASP311
|
3.7
|
27.6
|
1.0
|
CA
|
D:ASP304
|
4.0
|
28.6
|
1.0
|
OD2
|
D:ASP311
|
4.1
|
27.1
|
1.0
|
N
|
D:ASP311
|
4.1
|
28.5
|
1.0
|
N
|
D:ILE313
|
4.2
|
27.6
|
1.0
|
CA
|
D:ILE313
|
4.3
|
27.1
|
1.0
|
CA
|
D:LEU309
|
4.4
|
28.2
|
1.0
|
CB
|
D:ASP304
|
4.4
|
29.0
|
1.0
|
N
|
D:ALA310
|
4.4
|
28.8
|
1.0
|
CB
|
D:ASP307
|
4.5
|
27.1
|
1.0
|
N
|
D:LEU309
|
4.5
|
28.2
|
1.0
|
CB
|
D:LEU309
|
4.5
|
27.8
|
1.0
|
OD2
|
D:ASP304
|
4.5
|
29.0
|
1.0
|
CA
|
D:ALA310
|
4.5
|
29.1
|
1.0
|
N
|
D:VAL314
|
4.6
|
32.0
|
1.0
|
OD2
|
D:ASP315
|
4.6
|
26.1
|
1.0
|
O
|
D:HOH900
|
4.6
|
23.8
|
1.0
|
N
|
D:ASP315
|
4.6
|
26.4
|
1.0
|
N
|
D:ALA305
|
4.6
|
29.1
|
1.0
|
CB
|
D:ILE313
|
4.7
|
26.8
|
1.0
|
CA
|
D:VAL314
|
4.7
|
27.0
|
1.0
|
CB
|
D:ASP311
|
4.8
|
27.9
|
1.0
|
C
|
D:ALA310
|
4.8
|
28.9
|
1.0
|
CA
|
D:ASP311
|
4.9
|
28.4
|
1.0
|
CA
|
D:ALA305
|
5.0
|
29.1
|
1.0
|
N
|
D:GLY312
|
5.0
|
28.5
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6qgb
Go back to
Calcium Binding Sites List in 6qgb
Calcium binding site 5 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid
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 Benzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca702
b:23.1
occ:1.00
|
O
|
E:ILE313
|
2.3
|
28.9
|
1.0
|
OD1
|
E:ASP311
|
2.3
|
29.9
|
1.0
|
O
|
E:HOH837
|
2.4
|
34.9
|
1.0
|
O
|
E:LEU309
|
2.4
|
31.1
|
1.0
|
OD1
|
E:ASP304
|
2.4
|
35.4
|
1.0
|
O
|
E:ASP304
|
2.5
|
30.3
|
1.0
|
OD1
|
E:ASP307
|
2.6
|
30.2
|
1.0
|
OD2
|
E:ASP307
|
2.6
|
31.4
|
1.0
|
CG
|
E:ASP307
|
2.9
|
29.6
|
1.0
|
CG
|
E:ASP311
|
3.4
|
30.1
|
1.0
|
C
|
E:ASP304
|
3.5
|
30.6
|
1.0
|
C
|
E:ILE313
|
3.5
|
28.4
|
1.0
|
C
|
E:LEU309
|
3.7
|
31.7
|
1.0
|
CG
|
E:ASP304
|
3.7
|
31.7
|
1.0
|
OD2
|
E:ASP311
|
3.9
|
29.8
|
1.0
|
N
|
E:ASP311
|
4.0
|
31.2
|
1.0
|
CA
|
E:ASP304
|
4.0
|
30.3
|
1.0
|
N
|
E:ILE313
|
4.2
|
29.0
|
1.0
|
OD2
|
E:ASP315
|
4.2
|
28.3
|
1.0
|
CA
|
E:ILE313
|
4.4
|
28.4
|
1.0
|
CB
|
E:ASP307
|
4.4
|
29.6
|
1.0
|
CB
|
E:ASP304
|
4.5
|
30.7
|
1.0
|
CA
|
E:LEU309
|
4.5
|
31.9
|
1.0
|
N
|
E:VAL314
|
4.5
|
28.0
|
1.0
|
N
|
E:ALA305
|
4.6
|
31.3
|
1.0
|
OD2
|
E:ASP304
|
4.6
|
30.9
|
1.0
|
CB
|
E:LEU309
|
4.6
|
31.5
|
1.0
|
CB
|
E:ASP311
|
4.6
|
30.7
|
1.0
|
N
|
E:LEU309
|
4.6
|
31.8
|
1.0
|
N
|
E:ALA310
|
4.6
|
32.3
|
1.0
|
N
|
E:ASP315
|
4.6
|
27.9
|
1.0
|
O
|
E:HOH934
|
4.6
|
19.0
|
1.0
|
CA
|
E:ALA310
|
4.6
|
32.2
|
1.0
|
CB
|
E:ILE313
|
4.7
|
28.2
|
1.0
|
CA
|
E:VAL314
|
4.7
|
28.0
|
1.0
|
CA
|
E:ASP311
|
4.8
|
31.0
|
1.0
|
C
|
E:ALA310
|
4.8
|
31.9
|
1.0
|
CA
|
E:ALA305
|
4.8
|
31.7
|
1.0
|
N
|
E:GLY312
|
4.9
|
30.3
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6qgb
Go back to
Calcium Binding Sites List in 6qgb
Calcium binding site 6 out
of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid
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 Benzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca702
b:25.4
occ:1.00
|
O
|
F:LEU309
|
2.3
|
27.8
|
1.0
|
OD1
|
F:ASP304
|
2.4
|
34.4
|
1.0
|
OD1
|
F:ASP311
|
2.4
|
27.5
|
1.0
|
O
|
F:ILE313
|
2.4
|
26.5
|
1.0
|
O
|
F:HOH814
|
2.5
|
30.6
|
1.0
|
OD2
|
F:ASP307
|
2.5
|
32.9
|
1.0
|
OD1
|
F:ASP307
|
2.6
|
27.6
|
1.0
|
O
|
F:ASP304
|
2.6
|
32.4
|
1.0
|
CG
|
F:ASP307
|
2.9
|
26.5
|
1.0
|
CG
|
F:ASP311
|
3.4
|
28.1
|
1.0
|
C
|
F:ASP304
|
3.5
|
27.5
|
1.0
|
C
|
F:LEU309
|
3.5
|
28.3
|
1.0
|
CG
|
F:ASP304
|
3.6
|
29.3
|
1.0
|
C
|
F:ILE313
|
3.6
|
26.4
|
1.0
|
OD2
|
F:ASP311
|
3.8
|
30.5
|
1.0
|
N
|
F:ASP311
|
4.0
|
28.8
|
1.0
|
CA
|
F:ASP304
|
4.1
|
27.5
|
1.0
|
OD2
|
F:ASP315
|
4.2
|
27.5
|
1.0
|
N
|
F:ILE313
|
4.2
|
27.2
|
1.0
|
CA
|
F:ILE313
|
4.4
|
26.6
|
1.0
|
CB
|
F:ASP307
|
4.4
|
26.3
|
1.0
|
CA
|
F:LEU309
|
4.4
|
28.3
|
1.0
|
CB
|
F:ASP304
|
4.4
|
28.7
|
1.0
|
N
|
F:ALA310
|
4.5
|
28.9
|
1.0
|
N
|
F:LEU309
|
4.5
|
28.0
|
1.0
|
OD2
|
F:ASP304
|
4.5
|
28.4
|
1.0
|
CA
|
F:ALA310
|
4.5
|
29.0
|
1.0
|
N
|
F:ALA305
|
4.5
|
28.0
|
1.0
|
CB
|
F:LEU309
|
4.6
|
28.1
|
1.0
|
CB
|
F:ASP311
|
4.6
|
28.4
|
1.0
|
O
|
F:HOH940
|
4.6
|
22.8
|
1.0
|
CB
|
F:ILE313
|
4.6
|
26.6
|
1.0
|
N
|
F:VAL314
|
4.6
|
26.1
|
1.0
|
N
|
F:ASP315
|
4.7
|
25.6
|
1.0
|
C
|
F:ALA310
|
4.7
|
31.2
|
1.0
|
CA
|
F:ASP311
|
4.7
|
28.7
|
1.0
|
CA
|
F:ALA305
|
4.8
|
28.1
|
1.0
|
CA
|
F:VAL314
|
4.8
|
26.2
|
1.0
|
N
|
F:GLY312
|
4.9
|
28.4
|
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 13:50:48 2024
|