SMTL ID : 3gb4.1

Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-trimer

Ligands

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 8 residues within 4Å: Chain A: C.49, H.51, R.52, A.54, C.68, Y.70, H.71, L.73 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.49, A:H.51, A:C.68, A:H.71 FES.5: 9 residues within 4Å: Chain B: C.49, H.51, R.52, A.54, C.68, Y.70, H.71, G.72, L.73 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.49, B:H.51, B:C.68, B:H.71 FES.10: 9 residues within 4Å: Chain C: C.49, H.51, R.52, A.54, C.68, Y.70, H.71, G.72, L.73 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.49, C:H.51, C:C.68, C:H.71

7 x CO: COBALT (II) ION(Non-covalent)

CO.2: 4 residues within 4Å: Chain A: N.154, H.160, H.165, D.294 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.160, A:H.165, A:D.294, A:D.294, H2O.1 CO.4: 1 residues within 4Å: Chain A: H.65 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.65, H2O.4 CO.6: 4 residues within 4Å: Chain B: N.154, H.160, H.165, D.294 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.160, B:H.165, B:D.294, B:D.294, H2O.7 CO.8: 1 residues within 4Å: Chain B: H.65 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.65, H2O.10 CO.9: 1 residues within 4Å: Chain B: H.83 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.83, H2O.10, H2O.13 CO.11: 4 residues within 4Å: Chain C: N.154, H.160, H.165, D.294 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.160, C:H.165, C:D.294, C:D.294, H2O.14 CO.12: 1 residues within 4Å: Chain C: H.65 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.65

2 x D3M: 3,6-dichloro-2-methoxybenzoic acid(Non-covalent)

D3M.3: 7 residues within 4Å: Chain A: L.202, N.230, I.232, G.249, H.251, L.282, W.285 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.202, A:W.285 Hydrogen bonds: A:N.230, A:N.230 Salt bridges: A:H.251 D3M.7: 11 residues within 4Å: Chain B: L.158, L.202, F.206, N.218, N.230, I.232, G.249, H.251, L.282, W.285, L.290 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.202, B:I.232, B:I.232, B:W.285 Hydrogen bonds: B:N.230, B:N.230 Salt bridges: B:H.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

D'Ordine, R.L. et al., Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase that catalyzes an exocyclic monooxygenation. J.Mol.Biol. (2009)

Release Date

2009-07-28

Peptides

DdmC: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DdmC

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