SMTL ID : 4xww.1

Crystal structure of RNase J complexed with RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x U- U- U- U- U- U- U: RNA (5'-D(UP*UP*UP*UP*UP*UP*U)-3')(Non-covalent)

U-U-U-U-U-U-U.1: 30 residues within 4Å: Chain A: I.30, F.52, H.86, E.87, D.88, H.153, T.211, F.245, A.246, S.247, G.270, R.271, S.272, Y.276, T.311, Q.316, M.318, A.319, V.320, R.323, I.347, P.348, H.377, S.379, G.380, H.381, H.403, H.408 Ligands: ZN.3, ZN.4 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U-U.2: 31 residues within 4Å: Chain B: I.30, F.52, H.86, E.87, D.88, H.153, T.211, T.244, F.245, A.246, S.247, G.270, R.271, S.272, Y.276, T.311, Q.316, M.318, A.319, V.320, R.323, A.330, I.347, P.348, H.377, S.379, G.380, H.381, H.403 Ligands: ZN.8, ZN.9 Protein-ligand interaction information (PLIP) not available

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.84, H.86, H.153, D.175 Ligands: U-U-U-U-U-U-U.1, ZN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.84, A:H.86, A:H.153, H2O.29 ZN.4: 6 residues within 4Å: Chain A: N.33, D.88, H.89, H.403 Ligands: U-U-U-U-U-U-U.1, ZN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.88, A:D.88, A:H.89, A:H.403, H2O.29 ZN.8: 6 residues within 4Å: Chain B: N.33, D.88, H.89, H.403 Ligands: U-U-U-U-U-U-U.2, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.88, B:D.88, B:H.89, B:H.403 ZN.9: 6 residues within 4Å: Chain B: H.84, H.86, H.153, D.175 Ligands: U-U-U-U-U-U-U.2, ZN.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.84, B:H.86, B:H.153

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 3 residues within 4Å: Chain A: G.59, D.61, D.456 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.59, A:D.456 MN.10: 2 residues within 4Å: Chain B: G.59, D.456 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.59, B:D.456

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.407 Chain B: P.346, V.354, N.355, V.358, Y.370, P.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.407, A:R.407 GOL.7: 6 residues within 4Å: Chain A: P.346, V.354, V.358, Y.370, P.371 Chain B: R.407 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:N.355 Hydrogen bonds: B:R.407, B:R.407

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J. Nucleic Acids Res. (2015)

Release Date

2015-12-16

Peptides

DR2417: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DR2417

Related Entries With Identical Sequence