SMTL ID : 1oyr.1

Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.86, G.124, T.125, R.126, D.181 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.124, A:T.125, A:R.126 Salt bridges: A:R.86, A:R.126 SO4.2: 3 residues within 4Å: Chain A: W.58, T.60, R.99 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.99 SO4.3: 5 residues within 4Å: Chain B: R.86, G.124, T.125, R.126, D.181 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.124, B:T.125, B:R.126 Salt bridges: B:R.86, B:R.126 SO4.4: 3 residues within 4Å: Chain B: W.58, T.60, R.99 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.99 SO4.5: 5 residues within 4Å: Chain C: R.86, G.124, T.125, R.126, D.181 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.124, C:T.125, C:R.126 Salt bridges: C:R.86, C:R.126 SO4.6: 3 residues within 4Å: Chain C: W.58, T.60, R.99 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.60 Salt bridges: C:R.99 SO4.7: 5 residues within 4Å: Chain D: R.86, G.124, T.125, R.126, D.181 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.124, D:T.125, D:R.126 Salt bridges: D:R.86, D:R.126 SO4.8: 3 residues within 4Å: Chain D: W.58, T.60, R.99 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.60 Salt bridges: D:R.99 SO4.9: 5 residues within 4Å: Chain E: R.86, G.124, T.125, R.126, D.181 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.124, E:T.125, E:R.126 Salt bridges: E:R.86, E:R.126 SO4.10: 3 residues within 4Å: Chain E: W.58, T.60, R.99 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.99 SO4.11: 5 residues within 4Å: Chain F: R.86, G.124, T.125, R.126, D.181 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.124, F:T.125, F:R.126 Salt bridges: F:R.86, F:R.126 SO4.12: 3 residues within 4Å: Chain F: W.58, T.60, R.99 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.99

3 x CD: CADMIUM ION(Non-covalent)

CD.13: 2 residues within 4Å: Chain A: H.3, E.179 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.3, A:E.179, A:E.179 CD.14: 1 residues within 4Å: Chain E: H.3 No protein-ligand interaction detected (PLIP) CD.15: 2 residues within 4Å: Chain D: H.3, E.179 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.179, D:E.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harlow, L.S. et al., Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. Protein Sci. (2004)

Release Date

2004-03-09

Peptides

Ribonuclease PH: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Ribonuclease PH

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