SMTL ID : 4cug.1

Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase in complex substrate fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.96 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.147, D.149, H.210 Ligands: OGA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.147, A:D.149, A:H.210 MN.5: 4 residues within 4Å: Chain B: H.147, D.149, H.210 Ligands: OGA.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.147, B:D.149, B:H.210

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

OGA.2: 13 residues within 4Å: Chain A: M.134, S.136, V.144, H.147, D.149, V.153, L.155, R.162, W.164, H.210, S.222 Chain C: R.11 Ligands: MN.1 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Salt bridges: C:R.11, A:R.162 Hydrogen bonds: A:S.136, A:S.222 OGA.6: 14 residues within 4Å: Chain B: M.134, S.136, V.144, H.147, D.149, V.153, L.155, R.162, W.164, H.210, T.220, S.222 Chain D: R.11 Ligands: MN.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.136, B:S.222 Salt bridges: B:R.162, D:R.11

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 7 residues within 4Å: Chain A: R.226, A.227, P.228, E.232, I.293, R.298 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.232 Hydrogen bonds: A:R.226, A:R.298 MPD.7: 4 residues within 4Å: Chain B: P.228, E.232, I.293, R.298 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.232 Hydrogen bonds: B:I.293

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: D.131, R.298 Chain C: M.12 Ligands: MPD.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.298

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

2014-04-16

Peptides

CUPIN 4 FAMILY PROTEIN: AB
50S RIBOSOMAL PROTEIN L16: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

CUPIN 4 FAMILY PROTEIN

50S RIBOSOMAL PROTEIN L16

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