SMTL ID : 1yt3.1

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: P.301, G.302, Y.303, R.304, K.305 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.302, A:Y.303, A:R.304, A:K.305 Salt bridges: A:R.304 SO4.2: 2 residues within 4Å: Chain A: R.331, N.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.335 Water bridges: A:R.331, A:R.331 Salt bridges: A:R.331 SO4.3: 3 residues within 4Å: Chain A: Q.336, K.345, Q.347 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.336, A:Q.347 Water bridges: A:K.345, A:N.348, A:N.348 Salt bridges: A:K.345 SO4.4: 3 residues within 4Å: Chain A: S.330, R.331 Ligands: SO4.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.331 Water bridges: A:A.329, A:R.332, A:R.332 Salt bridges: A:R.331 SO4.5: 1 residues within 4Å: Chain A: K.308 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.308 SO4.6: 3 residues within 4Å: Chain A: R.240, S.264, S.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.264, A:S.266 Water bridges: A:S.266 Salt bridges: A:R.240 SO4.7: 4 residues within 4Å: Chain A: R.189, S.330, R.332 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.189, A:S.330, A:S.330 Salt bridges: A:R.332

5 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.8: 5 residues within 4Å: Chain A: D.28, T.29, E.30, Q.45, D.155 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.28, A:E.30, A:D.155, H2O.7 ZN.9: 2 residues within 4Å: Chain A: D.28, D.85 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.28, A:D.85, H2O.7, H2O.7, H2O.8 ZN.10: 1 residues within 4Å: Chain A: S.14 No protein-ligand interaction detected (PLIP) ZN.11: 2 residues within 4Å: Chain A: W.223, K.227 No protein-ligand interaction detected (PLIP) ZN.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zuo, Y. et al., Crystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing. Structure (2005)

Release Date

2005-08-09

Peptides

Ribonuclease D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease D