SMTL ID : 2g8v.1

B. halodurans RNase H catalytic domain E188A mutant in complex with Mg2+ and RNA/DNA hybrid (reaction product)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x U- C- G- A- C- A: 5'-R(P*UP*CP*GP*AP*CP*A)-3'(Non-covalent)

U-C-G-A-C-A.1: 14 residues within 4Å: Chain A: N.51, E.55, D.78, S.79, Q.80, K.126, W.127, T.129 Ligands: DA-DT-DG-DT-DC-DG.2, DA-DT-DG-DT-DC-DG.2, DA-DT-DG-DT-DC-DG.2, DA-DT-DG-DT-DC-DG.2, DA-DT-DG-DT-DC-DG.2, MG.3 Protein-ligand interaction information (PLIP) not available

1 x DA- DT- DG- DT- DC- DG: 5'-D(*AP*TP*GP*TP*CP*G)-3'(Non-covalent)

DA-DT-DG-DT-DC-DG.2: 18 residues within 4Å: Chain A: N.23, P.24, T.50, N.51, N.52, M.53, T.81, K.84, W.85, K.92, S.93, T.94, L.95 Ligands: U-C-G-A-C-A.1, U-C-G-A-C-A.1, U-C-G-A-C-A.1, U-C-G-A-C-A.1, U-C-G-A-C-A.1 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.17, E.55, D.78 Ligands: U-C-G-A-C-A.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.17, A:E.55, A:D.78, H2O.2, H2O.3 MG.4: 1 residues within 4Å: Chain A: D.138 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.138, H2O.2, H2O.2, H2O.2, H2O.2

2 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 3 residues within 4Å: Chain A: Q.80, I.83, K.126 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.80, A:I.83, A:K.126 EOH.6: 3 residues within 4Å: Chain A: E.12, K.35, K.73 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.12 Hydrogen bonds: A:K.73, A:K.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowotny, M. et al., Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. Embo J. (2006)

Release Date

2006-04-25

Peptides

Ribonuclease H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease H

Related Entries With Identical Sequence