SMTL ID : 2g8i.1

B. halodurans RNase H catalytic domain D192N mutant in complex with Mn2+ and RNA/DNA hybrid (non-P nick at the active site)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: 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, MN.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: 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

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 5 residues within 4Å: Chain A: D.17, E.55, D.78 Ligands: U-C-G-A-C-A.1, MN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.17, A:E.55, A:D.78, A:D.78, H2O.1 MN.4: 4 residues within 4Å: Chain A: D.17, V.18, N.138 Ligands: MN.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.17, H2O.1, H2O.3, H2O.3, H2O.6 MN.5: 4 residues within 4Å: Chain A: K.90, R.97, D.109, E.112 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.109, A:E.112, H2O.6, H2O.9, H2O.10, H2O.12 MN.6: 2 residues within 4Å: Chain A: E.28, E.42 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.28, A:E.42, H2O.7, H2O.9

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 1 residues within 4Å: Chain A: Y.29 Ligand excluded by PLIP

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 4 residues within 4Å: Chain A: H.61, R.64, Y.65, E.68 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.64, A:E.68 Water bridges: A:R.64

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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