SMTL ID : 4bxf.1

60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.156, D.158, H.217 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.156, A:D.158, A:H.217, H2O.4 MN.3: 4 residues within 4Å: Chain B: H.156, D.158, H.217 Ligands: AKG.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.156, B:D.158, B:H.217, H2O.11

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

AKG.2: 11 residues within 4Å: Chain A: Y.144, L.153, H.156, D.158, K.171, W.173, H.217, A.219, H.230, T.232 Ligands: MN.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.153 Water bridges: A:L.153, A:K.171, A:A.219 Salt bridges: A:K.171, A:H.217, A:H.230, A:H.230 AKG.4: 11 residues within 4Å: Chain B: Y.144, L.153, H.156, D.158, K.171, W.173, H.217, A.219, H.230, T.232 Ligands: MN.3 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.153, B:W.173 Hydrogen bonds: B:G.152, B:L.153, B:T.232 Water bridges: B:Y.144, B:K.171 Salt bridges: B:K.171, B:H.217, B:H.230, B:H.230, D:H.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature (2014)

Release Date

2014-05-14

Peptides

BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA: AB
60S RIBOSOMAL PROTEIN L27A: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA

60S RIBOSOMAL PROTEIN L27A