SMTL ID : 4ncb.2 (1 other biounit)

Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

1 x DA- DC- DA- DA- DC- DC: 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'(Non-covalent)

DA-DC-DA-DA-DC-DC.1: 23 residues within 4Å: Chain A: Y.43, P.44, A.47, R.51, R.81, R.114, D.546, G.547, R.548, V.573, R.574, K.575, S.576, G.577, K.618 Chain B: G.11, G.12, T.13, T.14, G.15, T.16 Chain C: T.1 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.481, A:D.546 Water bridges: A:D.478, A:D.478, A:A.479, A:R.486 Salt bridges: A:K.575, A:K.664, A:R.668

1 x DT: THYMIDINE-5'-MONOPHOSPHATE(Non-covalent)

DT.2: 13 residues within 4Å: Chain A: N.195, Y.197, R.200, W.202, L.217, P.218, L.223, Y.226, H.227, R.232, I.254, P.255, H.256 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.223, A:Y.226 Hydrogen bonds: A:N.195, A:Y.197, A:H.256 Salt bridges: A:R.200, A:H.227, A:R.232 pi-Stacking: A:Y.226

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.478, D.660 Chain C: T.1 Ligands: MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.478, A:D.660, H2O.1, H2O.7 MG.4: 6 residues within 4Å: Chain A: D.478, A.479, D.546 Chain C: T.1 Ligands: DA-DC-DA-DA-DC-DC.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.478, A:D.546, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain A: K.457, V.685 Chain B: T.1, G.2, A.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.685, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheng, G. et al., Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-01-15

Peptides

Argonaute: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Argonaute

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