SMTL ID : 3tht.6 (7 other biounits)

Crystal structure and RNA binding properties of the RRM/AlkB domains in human ABH8, an enzyme catalyzing tRNA hypermodification, Northeast Structural Genomics Consortium Target HR5601B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.218, C.317, C.319, C.325 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.218, A:C.317, A:C.319, A:C.325 ZN.4: 4 residues within 4Å: Chain B: H.218, C.317, C.319, C.325 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.218, B:C.317, B:C.319, B:C.325

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: H.214, D.216, H.268 Ligands: AKG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.214, A:D.216, A:H.268 MN.5: 4 residues within 4Å: Chain B: H.214, D.216, H.268 Ligands: AKG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.214, B:D.216, B:H.268

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.3: 13 residues within 4Å: Chain A: N.203, Y.205, I.211, H.214, D.216, S.227, M.236, H.268, R.304, S.306, T.308, R.310 Ligands: MN.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.203, A:S.227, A:S.227, A:S.306 Salt bridges: A:H.214, A:R.304, A:R.310 AKG.6: 11 residues within 4Å: Chain B: N.203, Y.205, H.214, S.227, M.236, H.268, R.304, S.306, T.308, R.310 Ligands: MN.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.203, B:N.203, B:Y.205, B:S.227, B:S.227, B:S.306 Salt bridges: B:H.214, B:R.304, B:R.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pastore, C. et al., Crystal structure and RNA binding properties of the RNA recognition motif (RRM) and AlkB domains in human AlkB homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification. J.Biol.Chem. (2012)

Release Date

2011-11-02

Peptides

Alkylated DNA repair protein alkB homolog 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alkylated DNA repair protein alkB homolog 8

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