SMTL ID : 4cck.1

60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and N-oxalylglycine (NOG)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.159, D.161, H.224 Ligands: OGA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.159, A:D.161, A:H.224, H2O.5 MN.4: 4 residues within 4Å: Chain B: H.159, D.161, H.224 Ligands: OGA.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.159, B:D.161, B:H.224, H2O.14 MN.7: 4 residues within 4Å: Chain C: H.159, D.161, H.224 Ligands: OGA.8 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.159, C:D.161, C:H.224, H2O.21 MN.10: 4 residues within 4Å: Chain D: H.159, D.161, H.224 Ligands: OGA.11 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.159, D:D.161, D:H.224, H2O.29

4 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.2: 11 residues within 4Å: Chain A: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238 Ligands: MN.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.147, A:F.156, A:T.238 Water bridges: A:S.114, A:G.155, A:F.156, A:A.226 Salt bridges: A:K.174, A:H.224, A:H.236, A:H.236 OGA.5: 11 residues within 4Å: Chain B: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238 Ligands: MN.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.147, B:T.238 Water bridges: B:S.114, B:F.156, B:A.226 Salt bridges: B:K.174, B:H.224, B:H.236, B:H.236 OGA.8: 11 residues within 4Å: Chain C: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238 Ligands: MN.7 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:F.156 Water bridges: C:S.114, C:Y.147, C:Y.147, C:F.156, C:A.226 Salt bridges: C:K.174, C:H.224, C:H.236, C:H.236 OGA.11: 11 residues within 4Å: Chain D: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238 Ligands: MN.10 8 PLIP interactions: 8 interactions with chain D Water bridges: D:Y.147, D:Y.147, D:F.156, D:A.226 Salt bridges: D:K.174, D:H.224, D:H.236, D:H.236

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

EDO.3: 8 residues within 4Å: Chain A: G.139, S.140, N.245, R.320, F.324 Chain B: L.273, F.277, M.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.320 Water bridges: A:S.140, A:M.141, A:N.245, A:N.245 EDO.6: 8 residues within 4Å: Chain A: L.273, F.277, M.278 Chain B: G.139, S.140, N.245, R.320, F.324 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.245, B:R.320 Water bridges: B:S.140, B:S.140, B:M.141, B:N.245 EDO.9: 8 residues within 4Å: Chain C: G.139, S.140, N.245, R.320, F.324 Chain D: L.273, F.277, M.278 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.320 Water bridges: C:S.140, C:S.140, C:M.141, C:N.245, C:N.245, C:N.245 EDO.12: 7 residues within 4Å: Chain C: L.273, F.277 Chain D: G.139, S.140, N.245, R.320, F.324 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.320 Water bridges: D:S.140, D:M.141, D:N.245

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 NO66: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66

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