SMTL ID : 4bu2.1

60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-dimer

Ligands

4 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.156, D.158, H.217 Ligands: AKG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.156, A:D.158, A:H.217, H2O.3 NI.2: 2 residues within 4Å: Chain A: H.172, D.220 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.172, A:D.220, H2O.5 NI.8: 4 residues within 4Å: Chain B: H.156, D.158, H.217 Ligands: AKG.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.156, B:D.158, B:H.217, H2O.7 NI.9: 2 residues within 4Å: Chain B: H.172, D.220 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.172, B:D.220, H2O.10

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

AKG.3: 12 residues within 4Å: Chain A: Y.144, G.152, L.153, H.156, D.158, K.171, W.173, H.217, H.230, T.232 Ligands: NI.1, EDO.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.144 Hydrogen bonds: A:L.153 Water bridges: A:Y.144, A:Y.144, A:T.146, A:T.146, A:A.219 Salt bridges: A:K.171, A:H.217, A:H.230 AKG.10: 12 residues within 4Å: Chain B: Y.144, G.152, L.153, H.156, D.158, K.171, W.173, H.217, H.230, T.232 Ligands: NI.8, EDO.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.144 Hydrogen bonds: B:L.153, B:T.232 Water bridges: B:K.171, B:A.219 Salt bridges: B:K.171, B:H.217, B:H.230

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: E.129, K.130, F.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.129, A:K.130 EDO.5: 5 residues within 4Å: Chain A: N.142, Y.144, D.158, T.232 Ligands: AKG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.142 Water bridges: A:N.142 EDO.6: 3 residues within 4Å: Chain A: F.120, K.121, D.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.122 EDO.7: 6 residues within 4Å: Chain A: S.137, L.138, N.239, M.307, D.310, F.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.137, A:L.138 EDO.11: 3 residues within 4Å: Chain B: E.129, K.130, F.345 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.129, B:K.130 EDO.12: 5 residues within 4Å: Chain B: N.142, Y.144, D.158, T.232 Ligands: AKG.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.142, B:Y.144 Water bridges: B:N.142 EDO.13: 3 residues within 4Å: Chain B: F.120, K.121, D.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.122 EDO.14: 6 residues within 4Å: Chain B: S.137, L.138, N.239, M.307, D.310, F.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.137, B:L.138

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA

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