SMTL ID : 5ws2.1

Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, complex with RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x A- A- A- A- A: RNA (5'-R(P*AP*AP*AP*AP*A)-3')(Non-covalent)

A-A-A-A-A.1: 34 residues within 4Å: Chain A: M.37, L.59, D.60, Q.63, H.106, L.107, D.108, H.174, D.196, N.231, F.267, A.268, G.292, R.293, S.294, Y.298, R.320, T.343, E.348, P.349, G.350, A.351, N.376, I.378, P.379, T.383, H.406, S.408, G.409, H.410, H.432 Ligands: ZN.3, ZN.4, SO4.15 Protein-ligand interaction information (PLIP) not available A-A-A-A-A.2: 33 residues within 4Å: Chain B: M.37, L.59, D.60, Q.63, H.106, L.107, D.108, H.174, D.196, N.231, F.267, A.268, G.292, R.293, S.294, T.343, E.348, P.349, G.350, A.351, N.376, I.378, P.379, T.383, H.406, S.408, G.409, H.410, H.432, M.437 Ligands: ZN.8, ZN.9, SO4.14 Protein-ligand interaction information (PLIP) not available

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.108, H.109, D.196, H.432 Ligands: A-A-A-A-A.1, ZN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.108, A:H.109, A:D.196, A:H.432, H2O.1 ZN.4: 6 residues within 4Å: Chain A: H.104, H.106, H.174, D.196 Ligands: A-A-A-A-A.1, ZN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.104, A:H.106, A:H.174, A:D.196, H2O.1 ZN.8: 7 residues within 4Å: Chain B: N.40, D.108, H.109, D.196, H.432 Ligands: A-A-A-A-A.2, ZN.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.108, B:D.196, B:D.196, B:H.432, H2O.7 ZN.9: 6 residues within 4Å: Chain B: H.104, H.106, H.174, D.196 Ligands: A-A-A-A-A.2, ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.104, B:H.106, B:D.196, H2O.7

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

SO4.5: 2 residues within 4Å: Chain A: R.58, R.61 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.58, A:R.58 Salt bridges: A:R.58, A:R.61 SO4.6: 3 residues within 4Å: Chain A: H.74, R.119, F.144 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.74, A:R.119 SO4.7: 4 residues within 4Å: Chain A: G.233, N.235, R.413 Chain B: K.395 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.395, A:R.413 Water bridges: A:R.413 SO4.10: 2 residues within 4Å: Chain B: R.58, R.61 6 PLIP interactions: 6 interactions with chain B Water bridges: B:N.35, B:E.36, B:R.58, B:R.61 Salt bridges: B:R.58, B:R.61 SO4.11: 4 residues within 4Å: Chain B: H.74, H.118, R.119, F.144 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.118, B:R.119 SO4.12: 4 residues within 4Å: Chain A: K.395 Chain B: G.233, N.235, R.413 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:E.391, A:E.391 Salt bridges: A:K.395, B:R.413 Hydrogen bonds: B:G.233 SO4.13: 3 residues within 4Å: Chain B: H.245, K.249, F.280 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.245, B:K.249 SO4.14: 3 residues within 4Å: Chain B: S.319, R.320 Ligands: A-A-A-A-A.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.320 Water bridges: B:R.293, B:R.293 SO4.15: 4 residues within 4Å: Chain A: R.293, S.319, R.320 Ligands: A-A-A-A-A.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.320 Salt bridges: A:R.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family. Mol. Microbiol. (2017)

Release Date

2017-12-06

Peptides

Ribonuclease J: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonuclease J

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