SMTL ID : 4l2n.2 (1 other biounit)

Understanding Extradiol Dioxygenase Mechanism in NAD+ Biosynthesis by Viewing Catalytic Intermediates - ligand-free structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

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

FE2.1: 3 residues within 4Å: Chain A: H.51, E.57, H.95 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.51, A:E.57, A:H.95, H2O.1, H2O.1 FE2.2: 4 residues within 4Å: Chain A: C.125, C.128, C.162, C.165 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.125, A:C.128, A:C.162, A:C.165 FE2.5: 3 residues within 4Å: Chain B: H.51, E.57, H.95 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.51, B:E.57, B:H.95, H2O.5, H2O.5 FE2.6: 4 residues within 4Å: Chain B: C.125, C.128, C.162, C.165 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.125, B:C.128, B:C.162, B:C.165

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: P.97, R.99 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: P.97, R.99 Ligand excluded by PLIP

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 6 residues within 4Å: Chain A: V.132, H.133, D.158, K.159, R.161, P.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.133, A:K.159, A:R.161 TRS.8: 6 residues within 4Å: Chain B: V.132, H.133, D.158, K.159, R.161, P.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.133, B:K.159, B:R.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, F. et al., An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE. J.Biol.Chem. (2015)

Release Date

2015-05-06

Peptides

3-hydroxyanthranilate 3,4-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3-hydroxyanthranilate 3,4-dioxygenase

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