SMTL ID : 4py5.1

Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: N.79, E.80, S.216 Chain B: G.7, A.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.80, H2O.1, H2O.1

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

SO4.2: 4 residues within 4Å: Chain A: R.75, R.199, E.201, R.203 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.72, A:R.203, A:D.209 Salt bridges: A:R.75, A:R.199, A:R.203 SO4.3: 1 residues within 4Å: Chain A: K.251 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.251, A:K.251 Salt bridges: A:K.251 SO4.4: 3 residues within 4Å: Chain A: K.196, G.197, A.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.197 Water bridges: A:A.198, A:A.198 Salt bridges: A:K.196 SO4.5: 3 residues within 4Å: Chain A: K.54, G.55, R.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.55, A:R.56 Salt bridges: A:R.56 SO4.6: 6 residues within 4Å: Chain A: N.155, R.156, S.184, N.185, R.186 Chain C: C.17 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.155, A:N.185, A:N.185, A:R.186 Water bridges: A:N.153, A:R.156 Salt bridges: A:R.156 SO4.7: 3 residues within 4Å: Chain A: T.252, P.253, K.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.254 SO4.9: 5 residues within 4Å: Chain B: G.3 Chain C: G.14, C.15, A.16, C.17 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: R.199, L.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.200, A:L.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Figiel, M. et al., Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition. Nucleic Acids Res. (2014)

Release Date

2014-07-30

Peptides

Ribonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease