SMTL ID : 6llb.1

Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, in complex with 6 nt RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

A-A-A-A-A-A.1: 38 residues within 4Å: Chain A: M.37, L.59, D.60, Q.63, H.106, L.107, D.108, H.136, H.174, D.196, N.231, F.267, A.268, G.292, R.293, S.294, R.297, G.318, S.319, R.320, T.343, H.345, E.348, P.349, G.350, A.351, N.376, I.378, P.379, N.380, T.383, H.406, S.408, G.409, H.410, H.432 Ligands: ZN.3, ZN.4 Protein-ligand interaction information (PLIP) not available A-A-A-A-A-A.2: 38 residues within 4Å: Chain B: M.37, L.59, D.60, H.106, L.107, D.108, H.174, D.196, T.230, N.231, F.267, A.268, G.292, R.293, S.294, E.296, R.297, Y.298, G.318, S.319, R.320, T.343, H.345, E.348, P.349, G.350, A.351, N.376, I.378, P.379, H.406, S.408, G.409, H.410, H.432, M.437 Ligands: ZN.10, ZN.11 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-A.1, ZN.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.108, A:H.109, A:D.196, A:D.196, A:H.432 ZN.4: 7 residues within 4Å: Chain A: H.104, H.106, D.108, H.174, D.196 Ligands: A-A-A-A-A-A.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.104, A:H.106, A:H.174, A:D.196 ZN.10: 6 residues within 4Å: Chain B: D.108, H.109, D.196, H.432 Ligands: A-A-A-A-A-A.2, ZN.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.108, B:D.108, B:H.109, B:D.196, B:H.432 ZN.11: 7 residues within 4Å: Chain B: H.104, H.106, D.108, H.174, D.196 Ligands: A-A-A-A-A-A.2, ZN.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.104, B:H.174, B:D.196

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

SO4.5: 2 residues within 4Å: Chain A: R.58, R.61 2 PLIP interactions: 2 interactions with chain A 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: 3 residues within 4Å: Chain A: N.235, R.413 Chain B: E.391 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.235 Salt bridges: A:R.413, B:K.395 SO4.8: 2 residues within 4Å: Chain A: H.5, H.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.5, A:H.7 SO4.9: 4 residues within 4Å: Chain A: H.8, H.9, H.10, S.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.11, A:S.11 Salt bridges: A:H.8 SO4.12: 2 residues within 4Å: Chain B: R.58, R.61 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.58, B:R.61 SO4.13: 2 residues within 4Å: Chain B: H.118, R.119 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.118, B:R.119 SO4.14: 4 residues within 4Å: Chain A: K.395 Chain B: G.233, N.235, R.413 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.235 Salt bridges: B:R.413, A:K.395 SO4.15: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., A newly identified duplex RNA unwinding activity of archaeal RNase J depends on processive exoribonucleolysis coupled steric occlusion by its structural archaeal loops. Rna Biol. (2020)

Release Date

2020-01-01

Peptides

MPY-RNase J: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MPY-RNase J

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