SMTL ID : 5v0a.1

Crystal structure of human exonuclease 1 Exo1 (D225A) in complex with 5' recessed-end DNA (rVIII)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 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: 25 residues within 4Å: Chain A: G.2, L.7, Q.8, K.85, R.92, E.150, D.152, E.170, D.171, S.172, D.173, K.185 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.8, D5M.9 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.40 Hydrogen bonds: A:R.95, A:R.95, A:E.117, A:S.229, A:L.230, A:G.232, A:I.233, A:G.234, A:A.236, A:K.237 Water bridges: A:R.231, A:R.231 Salt bridges: A:K.37, A:R.231, A:R.231, A:K.237

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.2: 5 residues within 4Å: Chain A: D.152, D.171, D.173 Ligands: DC-DG-DA-DC-DT-DA-DG-DC-DG.1, MN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.152, A:D.171, A:D.173, H2O.2 MN.3: 6 residues within 4Å: Chain A: D.78, D.152, D.171 Ligands: DC-DG-DA-DC-DT-DA-DG-DC-DG.1, MN.2, D5M.9 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.152, H2O.1, H2O.1, H2O.1 MN.4: 3 residues within 4Å: Chain A: C.80, I.325, F.335 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.80, H2O.3 MN.5: 2 residues within 4Å: Chain A: E.302, D.303 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.303 MN.7: 3 residues within 4Å: Chain A: A.41, E.44 Chain B: C.11 No protein-ligand interaction detected (PLIP) MN.8: 2 residues within 4Å: Chain B: C.3 Ligands: DC-DG-DA-DC-DT-DA-DG-DC-DG.1 No protein-ligand interaction detected (PLIP)

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

NA.6: 5 residues within 4Å: Chain A: S.222, S.229, I.233, G.234 Chain B: A.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.229, A:S.229 Water bridges: A:Q.4

1 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.9: 7 residues within 4Å: Chain A: Y.32, H.36, R.92, R.96 Chain B: T.10 Ligands: DC-DG-DA-DC-DT-DA-DG-DC-DG.1, MN.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:E.89, A:R.92, A:R.92, A:R.96 Salt bridges: A:H.36, A:R.92, A:R.96 pi-Stacking: A:H.36, A:H.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-05-24

Peptides

Exonuclease 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Z

Exonuclease 1

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