SMTL ID : 2r7y.1

Selenium Derivatized RNA/DNA Hybrid in complex with RNase H CATALYTIC DOMAIN MUTANT D132N

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: 25 residues within 4Å: Chain A: D.10, V.11, G.12, S.13, Q.14, G.15, N.16, N.44, N.45, E.48, N.71, S.72, Q.73, T.74, K.119, W.120, T.122 Ligands: DA-DT-SDG-DT-DC-SDG.2, DA-DT-SDG-DT-DC-SDG.2, DA-DT-SDG-DT-DC-SDG.2, DA-DT-SDG-DT-DC-SDG.2, DA-DT-SDG-DT-DC-SDG.2, DA-DT-SDG-DT-DC-SDG.2, MG.4, MG.5 Protein-ligand interaction information (PLIP) not available

1 x DA- DT- SDG- DT- DC- SDG: DNA (5'-D(*DAP*DTP*(SDG)P*DTP*DCP*(SDG))-3')(Non-covalent)

DA-DT-SDG-DT-DC-SDG.2: 15 residues within 4Å: Chain A: N.16, P.17, T.43, N.44, N.45, T.74, W.78, S.86, T.87 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, PO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.45, A:S.86, A:T.87 Water bridges: A:Q.73

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain A: W.78, K.85 Ligands: DA-DT-SDG-DT-DC-SDG.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.77, A:K.77

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.10, E.48, N.71 Ligands: U-C-G-A-C-A.1, U-C-G-A-C-A.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.10, A:E.48, A:E.48 MG.5: 3 residues within 4Å: Chain A: D.10, D.131 Ligands: U-C-G-A-C-A.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.10, A:D.131, H2O.2, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, J.-S. et al., Selenium Derivatized RNA/DNA Hybrid in complex with RNase H CATALYTIC DOMAIN MUTANT D132N. To be Published

Release Date

2008-05-06

Peptides

Ribonuclease H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease H

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