SMTL ID : 7mxt.1

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (cmr)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

monomer

Ligands

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

DC-DG-DA-DC-DT-DA-DG-DC-DG.1: 24 residues within 4Å: Chain A: L.7, Q.8, Y.32, K.85, R.92, R.96, D.152, E.170, D.171, D.173, K.185, D.225 Chain B: C.1, G.2, C.3, T.4, A.5, G.6, T.7, C.8, G.9 Ligands: MN.2, MN.3, MN.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:E.117, A:R.121, A:S.229, A:G.232, A:I.233, A:I.233, A:G.234, A:L.235, A:A.236, A:K.237 Water bridges: A:R.121, A:R.121 Salt bridges: A:K.37, A:R.231

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

MN.2: 7 residues within 4Å: Chain A: D.152, D.171, D.173, D.225 Ligands: DC-DG-DA-DC-DT-DA-DG-DC-DG.1, MN.3, MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.152, A:D.171, A:D.173, H2O.1 MN.3: 6 residues within 4Å: Chain A: G.2, D.171, D.173, D.225 Ligands: DC-DG-DA-DC-DT-DA-DG-DC-DG.1, MN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, A:D.225, H2O.4 MN.5: 4 residues within 4Å: Chain A: D.78, D.152 Ligands: DC-DG-DA-DC-DT-DA-DG-DC-DG.1, MN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.152, H2O.1, H2O.1, H2O.4, H2O.4

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: S.222, S.229, I.233, G.234 Chain B: T.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.229, A:I.233 Water bridges: A:Q.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities. To Be Published

Release Date

2023-05-10

Peptides

Exonuclease 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Z

Exonuclease 1

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