SMTL ID : 5tdt.1

Oxygenated toluene intermediate in toluene 4-monooxygenase (T4moHD) after reaction in the crystal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

1 x PER: PEROXIDE ION(Non-covalent)

PER.1: 8 residues within 4Å: Chain A: E.104, A.107, E.134, E.197, E.231 Ligands: MBN.2, FE.5, FE.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.134 Water bridges: A:T.201

5 x MBN: TOLUENE(Non-covalent)

MBN.2: 11 residues within 4Å: Chain A: I.100, G.103, E.104, A.107, F.176, F.196, E.197, T.201 Ligands: PER.1, FE.5, FE.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.100, A:A.107, A:F.176, A:T.201 pi-Stacking: A:F.196 MBN.3: 12 residues within 4Å: Chain A: V.271, Y.331, G.334, V.335, W.338, P.394, I.402, P.403, V.405 Chain C: F.14, L.15 Ligands: MBN.4 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.271, A:Y.331, A:V.335, A:W.338, A:P.394, A:I.402, A:P.403, A:P.403, A:V.405, C:F.14, C:L.15 MBN.4: 8 residues within 4Å: Chain A: W.167, W.338, T.341, L.393, P.394, P.403, M.471 Ligands: MBN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.167, A:L.393, A:P.394, A:P.403 pi-Stacking: A:W.167 MBN.7: 10 residues within 4Å: Chain D: W.167, W.338, T.341, L.393, P.394, V.396, P.403, I.450, M.471 Ligands: MBN.8 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.167, D:W.167, D:W.338, D:T.341, D:L.393, D:P.394, D:V.396, D:P.403, D:I.450 MBN.8: 13 residues within 4Å: Chain D: W.167, V.271, Y.331, G.334, V.335, W.338, P.394, I.402, P.403, V.405 Chain G: F.14, L.15 Ligands: MBN.7 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain G Hydrophobic interactions: D:W.167, D:V.271, D:Y.331, D:V.335, D:W.338, D:P.394, D:I.402, D:P.403, D:P.403, D:V.405, G:F.14, G:L.15

4 x FE: FE (III) ION(Non-covalent)

FE.5: 6 residues within 4Å: Chain A: E.104, E.134, H.137 Ligands: PER.1, MBN.2, FE.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.104, A:E.134, A:H.137, H2O.2, H2O.3 FE.6: 7 residues within 4Å: Chain A: E.134, E.197, E.231, H.234 Ligands: PER.1, MBN.2, FE.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.134, A:E.197, A:E.231, A:H.234, H2O.2 FE.9: 4 residues within 4Å: Chain D: E.104, E.134, H.137 Ligands: FE.10 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.104, D:E.134, D:H.137, H2O.34, H2O.40, H2O.46 FE.10: 5 residues within 4Å: Chain D: E.134, E.197, E.231, H.234 Ligands: FE.9 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.134, D:E.197, D:E.231, D:H.234, H2O.34, H2O.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Acheson, J.F. et al., In-crystal reaction cycle of a toluene-bound diiron hydroxylase. Nature (2017)

Release Date

2017-03-22

Peptides

Toluene-4-monooxygenase system protein A: AD
Toluene-4-monooxygenase system protein E: BF
Toluene-4-monooxygenase system protein B: CG
Toluene-4-monooxygenase system protein D: EH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

F
F

C
C

G
G

E
E

H
H

Toluene-4-monooxygenase system protein A

Toluene-4-monooxygenase system protein E

Toluene-4-monooxygenase system protein B

Toluene-4-monooxygenase system protein D

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