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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:

Potassium (K) 3 atoms

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

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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

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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.
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