SMTL ID : 3twh.1

Selenium Derivatized RNA/DNA Hybrid in complex with RNase H Catalytic Domain D132N Mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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.13, V.14, G.15, S.16, Q.17, G.18, N.19, N.47, N.48, E.51, N.74, S.75, Q.76, T.77, K.122, W.123, T.125 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.3, MG.4 Protein-ligand interaction information (PLIP) not available

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

DA-DT-SDG-DT-DC-SDG.2: 16 residues within 4Å: Chain A: N.19, P.20, T.46, N.47, N.48, T.77, W.81, K.88, S.89, T.90 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, PO4.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.48, A:S.89, A:T.90, A:L.91 Water bridges: A:Q.76, A:T.77

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.13, D.134 Ligands: U-C-G-A-C-A.1, U-C-G-A-C-A.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.13, A:D.134, H2O.2, H2O.2, H2O.5 MG.4: 5 residues within 4Å: Chain A: D.13, E.51, N.74 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.13, A:E.51, A:E.51

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

PO4.5: 3 residues within 4Å: Chain A: W.81, K.88 Ligands: DA-DT-SDG-DT-DC-SDG.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.88 Salt bridges: A:K.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abdur, R. et al., Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides. Acta Crystallogr.,Sect.D (2014)

Release Date

2012-10-03

Peptides

Ribonuclease H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease H

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