SMTL ID : 3vca.1

Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-trimer

Ligands

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

FES.1: 10 residues within 4Å: Chain A: C.86, H.88, R.89, G.90, S.91, C.106, Y.108, H.109, Q.110, W.111 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.86, A:H.88, A:C.106, A:H.109 FES.5: 10 residues within 4Å: Chain B: C.86, H.88, R.89, G.90, S.91, C.106, Y.108, H.109, Q.110, W.111 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.86, B:H.88, B:C.106, B:H.109 FES.9: 10 residues within 4Å: Chain C: C.86, H.88, R.89, G.90, S.91, C.106, Y.108, H.109, Q.110, W.111 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.86, C:H.88, C:C.106, C:H.109

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

FE.2: 4 residues within 4Å: Chain A: N.198, H.204, H.209, D.360 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.209, A:D.360, H2O.287, H2O.353, H2O.360 FE.6: 4 residues within 4Å: Chain B: N.198, H.204, H.209, D.360 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.209, B:D.360, H2O.897, H2O.963, H2O.970 FE.10: 4 residues within 4Å: Chain C: N.198, H.204, H.209, D.360 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.209, C:D.360, H2O.1507, H2O.1573, H2O.1580

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: R.14, R.15, L.16, F.19, E.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.14, A:L.16, A:L.16 GOL.7: 5 residues within 4Å: Chain B: R.14, R.15, L.16, F.19, E.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.14, B:L.16, B:L.16 GOL.11: 5 residues within 4Å: Chain C: R.14, R.15, L.16, F.19, E.22 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.14, C:L.16, C:L.16

3 x PRO: PROLINE(Non-covalent)

PRO.4: 6 residues within 4Å: Chain A: T.61, L.62, E.68, L.92, K.95, R.97 5 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: P.4, A:E.68, A:K.95, C:Q.369 Water bridges: A:L.62 PRO.8: 6 residues within 4Å: Chain B: T.61, L.62, E.68, L.92, K.95, R.97 5 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: P.8, B:E.68, B:K.95, A:Q.369 Water bridges: B:L.62 PRO.12: 6 residues within 4Å: Chain C: T.61, L.62, E.68, L.92, K.95, R.97 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: C:E.68, C:K.95, B:Q.369, P.12 Water bridges: C:L.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daughtry, K.D. et al., Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman, and UV-Visible Spectroscopic Analysis of a Rieske-Type Demethylase. J.Am.Chem.Soc. (2012)

Release Date

2012-02-08

Peptides

Ring-hydroxylating dioxygenase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Ring-hydroxylating dioxygenase

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