SMTL ID : 4blu.2 (1 other biounit)

Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 10 residues within 4Å: Chain A: N.12, A.14, D.15, K.18, D.164, W.195, M.235 Ligands: GOL.2, PEG.5, EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.12, A:D.15, A:D.15, A:K.18

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.18, G.44, Y.48, D.164 Ligands: TRS.1, EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.18, A:Y.48 Water bridges: A:K.18, A:Y.48

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: Y.184, K.185, G.215 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.215, A:R.217 PEG.4: 3 residues within 4Å: Chain A: S.262, K.263, P.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.263 PEG.5: 4 residues within 4Å: Chain A: S.7, F.8, H.9 Ligands: TRS.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.8

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

EDO.6: 8 residues within 4Å: Chain A: S.7, A.10, D.15, Y.48, Y.97, P.98 Ligands: TRS.1, GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.7, A:P.98 Water bridges: A:K.18 EDO.7: 2 residues within 4Å: Chain A: P.246, W.247 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.247 Water bridges: A:S.28, A:S.28, A:K.32, A:P.245 EDO.8: 2 residues within 4Å: Chain A: K.32, R.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.32, A:K.32, A:R.158 EDO.9: 2 residues within 4Å: Chain A: R.109, Q.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.111 EDO.10: 4 residues within 4Å: Chain A: P.166, E.168, M.169, D.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.168 Water bridges: A:D.172 EDO.11: 3 residues within 4Å: Chain A: E.182, K.185, R.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.185, A:R.186 Water bridges: A:E.182 EDO.12: 3 residues within 4Å: Chain A: E.250, S.275, W.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.250, A:W.276, A:W.276 Water bridges: A:E.250 EDO.13: 2 residues within 4Å: Chain A: L.106 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.108 EDO.14: 3 residues within 4Å: Chain A: H.87, R.90 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.87, A:R.90

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.15: 3 residues within 4Å: Chain A: R.47, H.87, F.88 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.105, A:R.105, A:R.105 Salt bridges: A:R.47, A:H.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Punekar, A.S. et al., Structural and Functional Insights Into the Molecular Mechanism of Rrna M6A Methyltransferase Rlmj. Nucleic Acids Res. (2013)

Release Date

2013-08-21

Peptides

RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J

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