SMTL ID : 5haa.1

Crystal structure of mpy-RNase J, an archaeal RNase J from Methanolobus psychrophilus R15

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.108, H.109, D.196, H.410, H.432 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.108, A:D.196, A:D.196, A:H.432, H2O.1 ZN.2: 6 residues within 4Å: Chain A: H.104, H.106, D.108, H.174, D.196 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.104, A:H.106, A:H.174, A:D.196 ZN.7: 6 residues within 4Å: Chain B: H.104, H.106, D.108, H.174, D.196 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.104, B:H.106, B:H.174, B:D.196 ZN.8: 5 residues within 4Å: Chain B: D.108, H.109, D.196, H.432 Ligands: ZN.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.108, B:D.108, B:D.196, B:D.196, B:H.432 ZN.14: 6 residues within 4Å: Chain C: D.108, H.109, D.196, H.410, H.432 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.108, C:D.196, C:D.196, C:H.432, H2O.1 ZN.15: 6 residues within 4Å: Chain C: H.104, H.106, D.108, H.174, D.196 Ligands: ZN.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.104, C:H.106, C:H.174, C:D.196 ZN.20: 6 residues within 4Å: Chain D: H.104, H.106, D.108, H.174, D.196 Ligands: ZN.21 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.104, D:H.106, D:H.174, D:D.196 ZN.21: 5 residues within 4Å: Chain D: D.108, H.109, D.196, H.432 Ligands: ZN.20 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.108, D:D.108, D:D.196, D:D.196, D:H.432

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

SO4.3: 5 residues within 4Å: Chain A: N.376, H.406, S.408, G.409, H.410 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: T.266, F.267, A.268, S.269, S.294, T.343, H.345 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: G.292, R.293, S.294, T.343, A.351, V.352 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: R.293, G.318, S.319, R.320 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain B: N.376, H.406, S.408, G.409, H.410 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain B: T.266, F.267, A.268, S.269, T.343, H.345 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: G.292, R.293, S.294, T.343, A.351 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: R.293, S.319, R.320 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: D.403 Chain B: G.233, N.235, R.413 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain C: N.376, H.406, S.408, G.409, H.410 Ligand excluded by PLIP SO4.17: 7 residues within 4Å: Chain C: T.266, F.267, A.268, S.269, S.294, T.343, H.345 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain C: G.292, R.293, S.294, T.343, A.351, V.352 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: R.293, G.318, S.319, R.320 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain D: N.376, H.406, S.408, G.409, H.410 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain D: T.266, F.267, A.268, S.269, T.343, H.345 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain D: G.292, R.293, S.294, T.343, A.351 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: R.293, S.319, R.320 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: D.403 Chain D: G.233, N.235, R.413 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Molecular insights into catalysis and processive exonucleolytic mechanisms of prokaryotic RNase J revealing striking parallels with that of eukaryotic Xrn1. To Be Published

Release Date

2017-01-04

Peptides

Ribonuclease J: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Ribonuclease J