SMTL ID : 5k73.2 (4 other biounits)

as-isolated Dbr1 with Fe(II) and Zn(II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

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

FE2.1: 6 residues within 4Å: Chain A: D.47, N.92, H.182, H.232 Ligands: ZN.2, OH.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.47, A:H.182, A:H.232, OH.6

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.16, H.18, D.47, H.234 Ligands: FE2.1, OH.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.16, A:H.18, A:D.47, A:H.234, OH.6

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: R.52, N.97, H.101, P.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.97 Water bridges: A:R.52, A:R.52, A:D.56 Salt bridges: A:R.52, A:H.101 SO4.4: 5 residues within 4Å: Chain A: K.61, I.134, K.136, F.157, H.158 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.61, A:K.136, A:H.158 SO4.5: 3 residues within 4Å: Chain A: R.308, T.309, K.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.310 Salt bridges: A:K.310

1 x OH: HYDROXIDE ION(Non-covalent)

OH.6: 6 residues within 4Å: Chain A: H.18, D.47, H.232, H.234 Ligands: FE2.1, ZN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, N.E. et al., The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-12-07

Peptides

RNA lariat debranching enzyme, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

RNA lariat debranching enzyme, putative

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