SMTL ID : 3i3m.1

Crystal Structure of AlkB in complex with Mn(II), 2-oxoglutarate and methylated trinucleotide T-meC-T

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x DT- ME6- DT: DNA (5'-D(P*TP*(ME6)P*T)-3')(Non-covalent)

DT-ME6-DT.1: 19 residues within 4Å: Chain A: T.41, P.42, G.43, Y.45, T.46, M.47, M.51, W.59, Y.66, L.108, L.118, S.119, L.120, H.121, Q.122, D.125, R.151, R.200 Ligands: AKG.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.66, A:H.121 Hydrogen bonds: A:Y.66, A:Q.122, A:R.151 Water bridges: A:K.124 pi-Stacking: A:H.121

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

AKG.2: 15 residues within 4Å: Chain A: L.108, N.110, Y.112, L.118, H.121, D.123, S.135, H.177, I.179, R.194, N.196, T.198, R.200 Ligands: DT-ME6-DT.1, MN.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.118, A:I.179 Hydrogen bonds: A:N.110, A:Y.112, A:S.135, A:S.135 Water bridges: A:N.196, A:R.200, A:R.200 Salt bridges: A:H.121, A:R.194, A:R.200

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

MN.3: 4 residues within 4Å: Chain A: H.121, D.123, H.177 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.121, A:D.123, A:H.177, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, B. et al., Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-08-25

Peptides

Alpha-ketoglutarate-dependent dioxygenase alkB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-ketoglutarate-dependent dioxygenase alkB

Related Entries With Identical Sequence