SMTL ID : 7fhr.1

Crystal Structure of a Rieske Oxygenase from Cupriavidus metallidurans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-trimer

Ligands

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: R.6, N.9, E.10, D.363 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.9 EDO.2: 5 residues within 4Å: Chain A: R.407, W.408, E.426, M.429, R.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.426 EDO.3: 5 residues within 4Å: Chain A: H.2, L.369, G.370, D.373, T.374 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: R.48, H.268, E.314, P.315 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain B: R.6, N.9, E.10, D.363 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.9 EDO.11: 5 residues within 4Å: Chain B: R.407, W.408, E.426, M.429, R.430 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.426 EDO.12: 5 residues within 4Å: Chain B: H.2, L.369, G.370, D.373, T.374 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain B: R.48, H.268, E.314, P.315 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain C: R.6, N.9, E.10, D.363 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.9 EDO.20: 5 residues within 4Å: Chain C: R.407, W.408, E.426, M.429, R.430 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.426 EDO.21: 5 residues within 4Å: Chain C: H.2, L.369, G.370, D.373, T.374 No protein-ligand interaction detected (PLIP) EDO.26: 4 residues within 4Å: Chain C: R.48, H.268, E.314, P.315 No protein-ligand interaction detected (PLIP)

3 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 9 residues within 4Å: Chain A: E.178, H.183, A.184, H.188, R.235, N.237, V.247, D.351 Ligands: FE2.7 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:V.247, A:V.247 Hydrogen bonds: A:E.178, A:N.237 Water bridges: A:G.177, A:E.178, A:R.235 Salt bridges: A:H.183, A:H.188, A:R.235 GLU.13: 9 residues within 4Å: Chain B: E.178, H.183, A.184, H.188, R.235, N.237, V.247, D.351 Ligands: FE2.16 12 PLIP interactions: 10 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:V.247, B:V.247 Hydrogen bonds: B:E.178, B:N.237, E.13, E.13 Water bridges: B:G.177, B:E.178, B:R.235 Salt bridges: B:H.183, B:H.188, B:R.235 GLU.22: 9 residues within 4Å: Chain C: E.178, H.183, A.184, H.188, R.235, N.237, V.247, D.351 Ligands: FE2.25 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:V.247, C:V.247 Hydrogen bonds: C:E.178, C:N.237 Water bridges: C:G.177, C:E.178, C:R.235 Salt bridges: C:H.183, C:H.188, C:R.235

3 x GLY: GLYCINE(Non-covalent)

GLY.5: 2 residues within 4Å: Chain A: R.82, R.89 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.89 GLY.14: 2 residues within 4Å: Chain B: R.82, R.89 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.89 GLY.23: 2 residues within 4Å: Chain C: R.82, R.89 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.89

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

FES.6: 10 residues within 4Å: Chain A: C.71, H.73, R.74, G.75, A.76, C.90, Y.92, H.93, G.94, W.95 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.71, A:H.73, A:C.90, A:H.93 FES.15: 10 residues within 4Å: Chain B: C.71, H.73, R.74, G.75, A.76, C.90, Y.92, H.93, G.94, W.95 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.71, B:H.73, B:C.90, B:H.93 FES.24: 10 residues within 4Å: Chain C: C.71, H.73, R.74, G.75, A.76, C.90, Y.92, H.93, G.94, W.95 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.71, C:H.73, C:C.90, C:H.93

3 x FE2: FE (II) ION(Non-covalent)

FE2.7: 4 residues within 4Å: Chain A: H.183, H.188, D.351 Ligands: GLU.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.183, A:H.188, A:D.351, GLU.4, GLU.4 FE2.16: 4 residues within 4Å: Chain B: H.183, H.188, D.351 Ligands: GLU.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.183, B:H.188, B:D.351, B:D.351 FE2.25: 4 residues within 4Å: Chain C: H.183, H.188, D.351 Ligands: GLU.22 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: C:H.183, C:H.188, C:D.351, GLU.22, GLU.22

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain A: T.70, C.71, H.73, R.74, G.75 Chain B: L.362, D.363, K.366, E.367 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.363, A:D.68, A:T.70 Hydrogen bonds: A:H.73 GOL.18: 9 residues within 4Å: Chain B: T.70, C.71, H.73, R.74, G.75 Chain C: L.362, D.363, K.366, E.367 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Water bridges: C:D.363, B:D.68, B:T.70 Hydrogen bonds: B:H.73 GOL.27: 9 residues within 4Å: Chain A: L.362, D.363, K.366, E.367 Chain C: T.70, C.71, H.73, R.74, G.75 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.73 Water bridges: C:D.68, C:T.70, A:D.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahto, J.K. et al., Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni. J.Biol.Chem. (2021)

Release Date

2021-12-15

Peptides

Putative Phthalate 4,5-dioxygenase, subunit alpha: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Putative Phthalate 4,5-dioxygenase, subunit alpha