SMTL ID : 2g8u.1

B. halodurans RNase H catalytic domain D132N mutant in complex with Mg2+ and RNA/DNA hybrid (non-P nick at the active site)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

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

U-C-G-A-C-A.1: 13 residues within 4Å: Chain A: N.51, E.55, N.78, Q.80, K.126, 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, MG.4 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: 19 residues within 4Å: Chain A: N.23, P.24, T.50, N.51, N.52, M.53, Q.80, 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, N.78 Ligands: U-C-G-A-C-A.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.17, A:E.55, H2O.1 MG.4: 4 residues within 4Å: Chain A: D.17, E.134, D.138 Ligands: U-C-G-A-C-A.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.17, A:D.138, H2O.1

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

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