SMTL ID : 1y44.1

Crystal structure of RNase Z

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.63, H.65, H.140, D.211 Ligands: ZN.2, PO4.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.63, A:H.65, A:H.140, A:D.211, H2O.3 ZN.2: 6 residues within 4Å: Chain A: D.67, H.68, D.211, H.269 Ligands: ZN.1, PO4.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.67, A:H.68, A:D.211, A:H.269, H2O.3

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain A: G.11, H.65, D.67, H.140, D.211, H.247, H.269 Ligands: ZN.1, ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.11 Salt bridges: A:H.65, A:H.140, A:H.247, A:H.269

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: H.48, F.299 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.48 GOL.5: 7 residues within 4Å: Chain A: R.54, K.55, I.56, E.57, R.79, D.86, E.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.56, A:R.79 GOL.7: 2 residues within 4Å: Chain B: P.291, N.292 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.292

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 7 residues within 4Å: Chain B: R.31, S.32, R.54, K.55, I.56, E.57, D.86 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.86 Water bridges: B:R.54, B:D.86 Salt bridges: B:R.31, B:K.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de la Sierra-Gallay, I.L. et al., Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature (2005)

Release Date

2005-01-25

Peptides

Ribonuclease Z: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonuclease Z

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