SMTL ID : 4zhn.1

Crystal Structure of AlkB T208A mutant protein in complex with Co(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

monomer

Ligands

1 x DT- MA7- DT: methylated trinucleotide DNA T-meA-T(Non-covalent)

DT-MA7-DT.1: 18 residues within 4Å: Chain A: T.41, Y.45, T.46, M.47, W.59, Y.66, L.108, K.117, L.118, S.119, L.120, H.121, Q.122, D.123, D.125, R.151, R.200 Ligands: AKG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.66, A:Q.122, A:D.125, A:R.151 Water bridges: A:K.124, A:K.124, A:R.151 pi-Stacking: A:W.59, A:H.121, A:H.121

1 x CO: COBALT (II) ION(Non-covalent)

CO.2: 4 residues within 4Å: Chain A: H.121, D.123, H.177 Ligands: AKG.3 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

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

AKG.3: 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, A.198, R.200 Ligands: DT-MA7-DT.1, CO.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.118, A:I.179 Hydrogen bonds: A:N.110, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hall, M.L. et al., DFT Studies of the Rate-Limiting Step in the Reaction Cycle of the Fe/2OG Dioxygenase AlkB and Related Experimental Studies. To be published

Release Date

2015-12-23

Peptides

Alpha-ketoglutarate-dependent dioxygenase AlkB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-ketoglutarate-dependent dioxygenase AlkB