SMTL ID : 5k73.4 (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.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.47, A:H.182, A:H.232, OH.7

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.7 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.7

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

SO4.3: 4 residues within 4Å: Chain A: R.52, N.97, H.101, P.148 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.97 Water bridges: A:R.52, A:R.52, A:R.52, A:R.52, A:P.148, A:P.148 Salt bridges: A:R.52, A:H.101 SO4.4: 4 residues within 4Å: Chain A: Q.165, S.300, I.301, S.302 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.300, A:I.301, A:S.302 Water bridges: A:Q.165, A:Q.165 SO4.5: 5 residues within 4Å: Chain A: I.134, K.136, V.154, F.157, H.158 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.61, A:K.136, A:H.158 SO4.6: 2 residues within 4Å: Chain A: S.174, Q.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.175, A:Q.175

1 x OH: HYDROXIDE ION(Non-covalent)

OH.7: 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
D

RNA lariat debranching enzyme, putative

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