SMTL ID : 3uld.1

High resolution structure of DNA/RNA hybrid in complex with RNase H catalytic domain D132N mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

U-C-G-A-C-A.1: 15 residues within 4Å: Chain A: N.51, E.55, N.78, S.79, Q.80, K.126, W.127, T.129 Ligands: DA-DT-DG-DT-DC-PGN.2, DA-DT-DG-DT-DC-PGN.2, DA-DT-DG-DT-DC-PGN.2, DA-DT-DG-DT-DC-PGN.2, DA-DT-DG-DT-DC-PGN.2, DA-DT-DG-DT-DC-PGN.2, MG.3 Protein-ligand interaction information (PLIP) not available

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

DA-DT-DG-DT-DC-PGN.2: 18 residues within 4Å: Chain A: N.23, P.24, T.50, N.51, N.52, 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 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.84

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.17, E.55, N.78 Ligands: U-C-G-A-C-A.1, MG.4 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, V.18, D.138 Ligands: MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.17, A:D.138, H2O.3, H2O.4 MG.5: 2 residues within 4Å: Chain A: R.64, W.114 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: Y.29, R.43 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gan, J.H. et al., RNA/DNA hybrid in complex with RNase H catalytic domain mutant D132N. To be Published

Release Date

2012-11-14

Peptides

Ribonuclease H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease H

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