SMTL ID : 4ccm.1

60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-4-4-mer

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.3 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.10 MN.8: 4 residues within 4Å: Chain E: H.159, D.161, H.224 Ligands: OGA.9 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.159, E:D.161, E:H.224, H2O.17 MN.11: 4 residues within 4Å: Chain F: H.159, D.161, H.224 Ligands: OGA.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.159, F:D.161, F:H.224, H2O.24

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: 10 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:F.156, A:T.238 Water bridges: A:Y.147, A:Y.147, A:F.156, A:A.226 Salt bridges: A:K.174, A:H.224, A:H.236, A:H.236, C:H.12 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:F.156, B:H.236 Water bridges: B:F.156, B:K.174, B:A.226 Salt bridges: B:K.174, B:H.224, B:H.236, B:H.236 OGA.9: 11 residues within 4Å: Chain E: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238 Ligands: MN.8 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:F.156 Water bridges: E:F.156, E:A.226 Salt bridges: E:K.174, E:H.224, E:H.236, E:H.236, G:H.12 OGA.12: 11 residues within 4Å: Chain F: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238 Ligands: MN.11 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:F.156, F:H.236, F:T.238 Water bridges: F:Y.147, F:F.156, F:K.174, F:A.226 Salt bridges: F:K.174, F:H.224, F:H.236, F:H.236

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

EDO.3: 3 residues within 4Å: Chain A: R.271 Chain B: E.43, R.44 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.271, B:E.43, B:R.44 EDO.6: 7 residues within 4Å: Chain A: G.139, S.140, N.245, R.320, F.324 Chain B: F.277, M.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.140, A:R.320 Water bridges: A:M.141, A:N.245, A:N.245 EDO.7: 7 residues within 4Å: Chain A: F.277, M.278 Chain B: G.139, S.140, N.245, R.320, F.324 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.140, B:R.320 Water bridges: B:N.245, B:N.245 EDO.10: 3 residues within 4Å: Chain E: R.271 Chain F: E.43, R.44 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.271, F:R.44 EDO.13: 7 residues within 4Å: Chain E: G.139, S.140, N.245, R.320, F.324 Chain F: F.277, M.278 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.140, E:R.320 Water bridges: E:M.141, E:N.245, E:N.245 EDO.14: 7 residues within 4Å: Chain E: F.277, M.278 Chain F: G.139, S.140, N.245, R.320, F.324 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.140, F:R.320 Water bridges: F:N.245, F: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: ABEF
60S RIBOSOMAL PROTEIN L8: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
C

D
D

G
C

H
D

BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66

60S RIBOSOMAL PROTEIN L8

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