SMTL ID : 3t3o.1

Molecular basis for the recognition and cleavage of RNA (CUGG) by the bifunctional 5'-3' exo/endoribonuclease RNase J

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x OMC- OMU- OMG- OMG- U: O2'methyl-RNA(Non-covalent)

OMC-OMU-OMG-OMG-U.1: 30 residues within 4Å: Chain A: I.29, F.51, D.60, L.61, D.87, T.247, F.248, A.249, S.250, H.251, G.273, R.274, S.275, T.314, S.316, Q.317, Q.319, M.321, S.322, V.323, R.326, I.350, P.351, N.353, H.380, S.382, G.383, H.384, H.406 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.159, A:S.159, A:G.383, A:R.274, A:S.275, A:T.314, A:V.323, A:S.250, A:Q.319, A:N.353, A:N.353 Salt bridges: A:H.251, A:H.380 pi-Cation interactions: A:R.274 Hydrophobic interactions: A:F.51 Water bridges: A:E.86 OMC-OMU-OMG-OMG-U.4: 30 residues within 4Å: Chain B: I.29, F.51, D.60, L.61, D.87, T.247, F.248, A.249, S.250, H.251, G.273, R.274, S.275, T.314, S.316, Q.317, Q.319, M.321, S.322, V.323, R.326, I.350, P.351, N.353, H.380, S.382, G.383, H.384, H.406 Ligands: ZN.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.159, B:S.159, B:G.383, B:R.274, B:S.275, B:T.314, B:V.323, B:S.250, B:Q.319, B:N.353, B:N.353 Salt bridges: B:H.251, B:H.380 pi-Cation interactions: B:R.274 Hydrophobic interactions: B:F.51 Water bridges: B:E.86

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.83, D.87, H.88, D.180, H.406 Ligands: OMC-OMU-OMG-OMG-U.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.87, A:H.88, A:D.180, A:H.406 ZN.5: 6 residues within 4Å: Chain B: H.83, D.87, H.88, D.180, H.406 Ligands: OMC-OMU-OMG-OMG-U.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.87, B:H.88, B:D.180, B:H.406

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: V.448, G.449, E.450 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.450, A:E.450 GOL.6: 3 residues within 4Å: Chain B: V.448, G.449, E.450 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.450, B:E.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dorleans, A. et al., Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5'-3' Exo/Endoribonuclease RNase J. Structure (2011)

Release Date

2011-10-19

Peptides

Metal dependent hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Metal dependent hydrolase

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