SMTL ID : 4n76.2 (1 other biounit)

Structure of Thermus thermophilus Argonaute bound to guide DNA and cleaved target DNA with Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: Q.433, K.457, V.685 Chain B: T.1, G.2, A.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.685 MN.2: 6 residues within 4Å: Chain A: D.478, A.479, E.512, D.546 Chain C: T.1 Ligands: MN.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.478, A:D.546 MN.3: 5 residues within 4Å: Chain A: D.478, D.546, D.660 Chain C: T.1 Ligands: MN.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.478, A:D.660

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

DT.4: 12 residues within 4Å: Chain A: N.195, Y.197, W.202, L.217, P.218, L.223, Y.226, H.227, R.232, I.254, P.255, H.256 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.217, A:Y.226 Hydrogen bonds: A:N.195, A:Y.197, A:P.218, A:H.256 Salt bridges: A:R.232

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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