Iodine in PDB 8h5l: Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Enzymatic activity of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
All present enzymatic activity of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis:
3.1.1.101;
Protein crystallography data
The structure of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis, PDB code: 8h5l
was solved by
S.H.Lee,
H.Seo,
K.-J.Kim,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.97 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.168,
51.546,
100.37,
90,
119.09,
90
|
R / Rfree (%)
|
15.5 /
18.5
|
Other elements in 8h5l:
The structure of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
(pdb code 8h5l). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the
Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis, PDB code: 8h5l:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iodine binding site 1 out
of 8 in 8h5l
Go back to
Iodine Binding Sites List in 8h5l
Iodine binding site 1 out
of 8 in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1203
b:40.1
occ:1.00
|
O
|
A:HOH1449
|
3.6
|
33.1
|
1.0
|
CA
|
A:TRP96
|
3.9
|
7.9
|
1.0
|
CE
|
A:LYS95
|
4.1
|
20.8
|
1.0
|
N
|
A:TRP96
|
4.2
|
7.9
|
1.0
|
CG
|
A:LYS95
|
4.3
|
14.3
|
1.0
|
CB
|
A:TRP96
|
4.3
|
8.3
|
1.0
|
CD
|
A:LYS95
|
4.3
|
17.3
|
1.0
|
O
|
A:HOH1496
|
4.4
|
42.2
|
1.0
|
O
|
A:HOH1335
|
4.4
|
34.4
|
1.0
|
C
|
A:LYS95
|
4.5
|
8.7
|
1.0
|
O
|
A:LYS95
|
4.5
|
9.7
|
1.0
|
O
|
A:HOH1381
|
4.5
|
12.9
|
1.0
|
CG2
|
A:THR242
|
4.7
|
8.9
|
1.0
|
CG
|
A:PRO99
|
4.7
|
11.0
|
1.0
|
O
|
A:HOH1471
|
4.7
|
18.7
|
1.0
|
O
|
A:HOH1652
|
4.7
|
33.7
|
1.0
|
CD
|
A:PRO99
|
4.9
|
10.0
|
1.0
|
O
|
A:HOH1658
|
5.0
|
25.0
|
1.0
|
CB
|
A:LYS95
|
5.0
|
12.1
|
1.0
|
|
Iodine binding site 2 out
of 8 in 8h5l
Go back to
Iodine Binding Sites List in 8h5l
Iodine binding site 2 out
of 8 in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1204
b:30.1
occ:1.00
|
O
|
A:HOH1519
|
3.1
|
24.5
|
1.0
|
K
|
A:K1201
|
3.2
|
24.8
|
1.0
|
N
|
A:SER58
|
3.6
|
13.6
|
0.5
|
N
|
A:SER58
|
3.6
|
12.4
|
0.5
|
OG
|
A:SER58
|
3.9
|
21.6
|
0.5
|
CE2
|
A:PHE55
|
4.1
|
10.7
|
1.0
|
CA
|
A:VAL57
|
4.1
|
10.9
|
1.0
|
CB
|
A:SER58
|
4.1
|
17.6
|
0.5
|
CD2
|
A:LEU137
|
4.2
|
13.2
|
1.0
|
O
|
A:THR56
|
4.3
|
11.5
|
1.0
|
CD2
|
A:PHE55
|
4.3
|
10.4
|
1.0
|
CB
|
A:SER58
|
4.4
|
14.3
|
0.5
|
C
|
A:VAL57
|
4.4
|
11.8
|
1.0
|
CD1
|
A:LEU137
|
4.4
|
11.7
|
1.0
|
O
|
A:HOH1363
|
4.4
|
35.0
|
1.0
|
CA
|
A:SER58
|
4.5
|
15.6
|
0.5
|
O
|
A:HOH1585
|
4.5
|
32.6
|
1.0
|
CG1
|
A:VAL57
|
4.6
|
11.3
|
1.0
|
CA
|
A:SER58
|
4.6
|
13.5
|
0.5
|
CB
|
A:VAL57
|
4.8
|
11.4
|
1.0
|
O
|
A:HOH1654
|
4.9
|
30.4
|
1.0
|
|
Iodine binding site 3 out
of 8 in 8h5l
Go back to
Iodine Binding Sites List in 8h5l
Iodine binding site 3 out
of 8 in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1205
b:22.9
occ:1.00
|
OG
|
A:SER92
|
2.7
|
12.6
|
0.5
|
O
|
A:HOH1664
|
3.2
|
33.5
|
1.0
|
N
|
A:ARG90
|
3.6
|
7.5
|
1.0
|
N
|
A:SER93
|
4.0
|
8.0
|
1.0
|
CB
|
A:SER92
|
4.0
|
10.3
|
0.5
|
CB
|
A:SER93
|
4.1
|
8.0
|
1.0
|
O
|
A:ARG90
|
4.1
|
6.4
|
1.0
|
CB
|
A:ARG90
|
4.2
|
9.7
|
1.0
|
CA
|
A:ALA89
|
4.3
|
7.6
|
1.0
|
CB
|
A:ALA89
|
4.3
|
7.9
|
1.0
|
CA
|
A:ARG90
|
4.3
|
8.3
|
1.0
|
CB
|
A:SER92
|
4.4
|
8.0
|
0.5
|
C
|
A:ARG90
|
4.4
|
7.2
|
1.0
|
C
|
A:ALA89
|
4.4
|
7.9
|
1.0
|
CA
|
A:SER93
|
4.4
|
8.0
|
1.0
|
OG
|
A:SER93
|
4.6
|
7.1
|
1.0
|
C
|
A:SER92
|
4.7
|
8.3
|
0.5
|
C
|
A:SER92
|
4.7
|
7.7
|
0.5
|
O
|
A:HOH1478
|
4.7
|
30.2
|
1.0
|
CA
|
A:SER92
|
4.7
|
9.2
|
0.5
|
N
|
A:SER92
|
4.8
|
8.5
|
0.5
|
N
|
A:SER92
|
4.8
|
7.8
|
0.5
|
CA
|
A:SER92
|
4.8
|
7.9
|
0.5
|
O
|
A:HOH1583
|
4.9
|
25.4
|
1.0
|
CG
|
A:ARG90
|
5.0
|
13.4
|
1.0
|
OG
|
A:SER92
|
5.0
|
8.0
|
0.5
|
|
Iodine binding site 4 out
of 8 in 8h5l
Go back to
Iodine Binding Sites List in 8h5l
Iodine binding site 4 out
of 8 in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I1201
b:32.2
occ:1.00
|
O
|
B:HOH1483
|
3.3
|
21.1
|
1.0
|
N
|
B:SER58
|
3.6
|
14.5
|
0.5
|
N
|
B:SER58
|
3.6
|
14.3
|
0.5
|
O
|
B:HOH1638
|
4.0
|
36.3
|
1.0
|
CB
|
B:SER58
|
4.1
|
16.4
|
0.5
|
CE2
|
B:PHE55
|
4.1
|
13.0
|
1.0
|
CA
|
B:VAL57
|
4.1
|
13.1
|
1.0
|
OG
|
B:SER58
|
4.2
|
16.7
|
0.5
|
CB
|
B:SER58
|
4.2
|
16.4
|
0.5
|
CD2
|
B:LEU137
|
4.3
|
14.0
|
1.0
|
O
|
B:THR56
|
4.3
|
12.8
|
1.0
|
CD2
|
B:PHE55
|
4.3
|
11.9
|
1.0
|
C
|
B:VAL57
|
4.4
|
13.2
|
1.0
|
CA
|
B:SER58
|
4.4
|
15.5
|
0.5
|
CG1
|
B:VAL57
|
4.5
|
14.0
|
1.0
|
CA
|
B:SER58
|
4.5
|
15.1
|
0.5
|
CD1
|
B:LEU137
|
4.5
|
13.3
|
1.0
|
O
|
B:HOH1625
|
4.8
|
32.5
|
1.0
|
CB
|
B:VAL57
|
4.8
|
13.6
|
1.0
|
|
Iodine binding site 5 out
of 8 in 8h5l
Go back to
Iodine Binding Sites List in 8h5l
Iodine binding site 5 out
of 8 in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I1202
b:42.7
occ:1.00
|
O
|
B:HOH1457
|
3.7
|
30.4
|
1.0
|
CA
|
B:TRP96
|
3.9
|
10.2
|
1.0
|
O
|
B:HOH1436
|
4.2
|
33.2
|
1.0
|
CG
|
B:LYS95
|
4.2
|
17.3
|
1.0
|
N
|
B:TRP96
|
4.3
|
10.6
|
1.0
|
CE
|
B:LYS95
|
4.3
|
24.2
|
1.0
|
CB
|
B:TRP96
|
4.3
|
11.2
|
1.0
|
CD
|
B:LYS95
|
4.3
|
21.4
|
1.0
|
O
|
B:HOH1373
|
4.5
|
16.2
|
1.0
|
C
|
B:LYS95
|
4.5
|
11.7
|
1.0
|
O
|
B:LYS95
|
4.5
|
9.9
|
1.0
|
O
|
B:HOH1395
|
4.6
|
42.8
|
1.0
|
OG1
|
B:THR242
|
4.6
|
11.1
|
0.5
|
O
|
B:HOH1499
|
4.7
|
24.4
|
1.0
|
CG
|
B:PRO99
|
4.7
|
13.2
|
1.0
|
O
|
B:HOH1634
|
4.8
|
30.9
|
1.0
|
NZ
|
B:LYS95
|
4.9
|
26.8
|
1.0
|
CD
|
B:PRO99
|
4.9
|
12.1
|
1.0
|
O
|
B:HOH1594
|
5.0
|
33.4
|
1.0
|
|
Iodine binding site 6 out
of 8 in 8h5l
Go back to
Iodine Binding Sites List in 8h5l
Iodine binding site 6 out
of 8 in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I1203
b:26.1
occ:1.00
|
OG
|
B:SER92
|
2.7
|
14.5
|
0.5
|
O
|
B:HOH1626
|
3.5
|
36.0
|
1.0
|
N
|
B:ARG90
|
3.5
|
10.2
|
1.0
|
O
|
B:HOH1456
|
3.8
|
40.4
|
1.0
|
N
|
B:SER93
|
3.9
|
10.1
|
1.0
|
O
|
B:HOH1554
|
4.0
|
40.3
|
1.0
|
CB
|
B:SER93
|
4.0
|
10.6
|
1.0
|
CB
|
B:SER92
|
4.1
|
12.7
|
0.5
|
O
|
B:ARG90
|
4.1
|
9.1
|
1.0
|
CB
|
B:ARG90
|
4.2
|
11.8
|
1.0
|
CB
|
B:ALA89
|
4.2
|
8.5
|
1.0
|
CA
|
B:ALA89
|
4.2
|
8.7
|
1.0
|
CA
|
B:ARG90
|
4.3
|
10.4
|
1.0
|
CB
|
B:SER92
|
4.4
|
11.2
|
0.5
|
C
|
B:ARG90
|
4.4
|
10.4
|
1.0
|
C
|
B:ALA89
|
4.4
|
9.0
|
1.0
|
CA
|
B:SER93
|
4.4
|
10.5
|
1.0
|
OG
|
B:SER93
|
4.6
|
10.5
|
1.0
|
C
|
B:SER92
|
4.7
|
10.9
|
0.5
|
C
|
B:SER92
|
4.7
|
10.3
|
0.5
|
CA
|
B:SER92
|
4.7
|
11.2
|
0.5
|
N
|
B:SER92
|
4.8
|
10.6
|
0.5
|
N
|
B:SER92
|
4.8
|
10.0
|
0.5
|
CA
|
B:SER92
|
4.8
|
10.2
|
0.5
|
O
|
B:HOH1550
|
4.9
|
29.0
|
1.0
|
CG
|
B:ARG90
|
5.0
|
16.6
|
1.0
|
OG
|
B:SER92
|
5.0
|
10.9
|
0.5
|
|
Iodine binding site 7 out
of 8 in 8h5l
Go back to
Iodine Binding Sites List in 8h5l
Iodine binding site 7 out
of 8 in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I1204
b:25.1
occ:1.00
|
OG
|
B:SER207
|
3.4
|
17.9
|
0.5
|
N
|
B:SER207
|
3.6
|
14.3
|
0.5
|
N
|
B:SER207
|
3.6
|
13.8
|
0.5
|
N
|
B:HIS237
|
3.8
|
15.0
|
1.0
|
O
|
B:HOH1309
|
3.9
|
38.1
|
1.0
|
CB
|
B:HIS237
|
4.0
|
11.7
|
1.0
|
O
|
B:HOH1545
|
4.1
|
37.7
|
1.0
|
CB
|
B:SER207
|
4.1
|
15.1
|
0.5
|
O
|
B:ASN205
|
4.2
|
20.6
|
1.0
|
CB
|
B:SER236
|
4.2
|
19.8
|
1.0
|
CA
|
B:ASP206
|
4.2
|
16.4
|
1.0
|
CB
|
B:SER207
|
4.2
|
16.6
|
0.5
|
O
|
B:HOH1431
|
4.3
|
31.5
|
1.0
|
CA
|
B:SER207
|
4.4
|
15.2
|
0.5
|
CA
|
B:SER207
|
4.4
|
14.4
|
0.5
|
C
|
B:ASP206
|
4.4
|
13.3
|
1.0
|
CA
|
B:SER236
|
4.4
|
18.0
|
1.0
|
OD1
|
B:ASP206
|
4.4
|
13.8
|
1.0
|
CA
|
B:HIS237
|
4.5
|
13.3
|
1.0
|
OG
|
B:SER207
|
4.5
|
15.6
|
0.5
|
N
|
B:ILE208
|
4.6
|
13.3
|
1.0
|
C
|
B:SER236
|
4.6
|
14.6
|
1.0
|
CG1
|
B:ILE208
|
4.7
|
15.8
|
1.0
|
CD1
|
B:ILE208
|
4.7
|
16.0
|
1.0
|
C
|
B:SER207
|
4.9
|
14.2
|
0.5
|
C
|
B:SER207
|
5.0
|
13.8
|
0.5
|
|
Iodine binding site 8 out
of 8 in 8h5l
Go back to
Iodine Binding Sites List in 8h5l
Iodine binding site 8 out
of 8 in the Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Crystal Structure of Petase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224 E/N233C/S242T/N246D/N275C/S282C/F284C Mutant From Ideonella Sakaiensis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:I1502
b:54.3
occ:1.00
|
O
|
E:HOH1714
|
3.6
|
32.6
|
1.0
|
CA
|
E:TRP96
|
3.9
|
13.3
|
1.0
|
CG
|
E:LYS95
|
4.2
|
23.1
|
1.0
|
N
|
E:TRP96
|
4.2
|
14.5
|
1.0
|
CD
|
E:LYS95
|
4.3
|
25.2
|
1.0
|
CE
|
E:LYS95
|
4.3
|
31.9
|
1.0
|
CB
|
E:TRP96
|
4.4
|
13.8
|
1.0
|
C
|
E:LYS95
|
4.5
|
16.1
|
1.0
|
O
|
E:LYS95
|
4.5
|
14.3
|
1.0
|
O
|
E:HOH1689
|
4.6
|
17.8
|
1.0
|
OG1
|
E:THR242
|
4.7
|
12.1
|
0.5
|
CG
|
E:PRO99
|
4.7
|
15.8
|
1.0
|
O
|
E:HOH1703
|
4.7
|
22.8
|
1.0
|
O
|
E:HOH1884
|
4.8
|
29.8
|
1.0
|
NZ
|
E:LYS95
|
4.9
|
35.4
|
1.0
|
CB
|
E:LYS95
|
5.0
|
19.7
|
1.0
|
|
Reference:
S.H.Lee,
H.Seo,
K.J.Kim.
A Case of Balance Engineering Exhibits Kinetic Relationship Between Mesophilic and Thermophilic Poly(Ethylene Terephthalate) Depolymerases. To Be Published.
Page generated: Mon Aug 12 02:46:10 2024
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