SMTL ID : 5v09.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.152, D.171, D.173 Chain C: C.2 Ligands: 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.2: 2 residues within 4Å: Chain A: C.80, I.325 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.80, H2O.3 MN.4: 2 residues within 4Å: Chain A: A.41 Chain B: C.11 No protein-ligand interaction detected (PLIP) MN.5: 5 residues within 4Å: Chain A: D.78, D.152 Chain C: A.1, C.2 Ligands: MN.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.152, H2O.1, H2O.1, H2O.2 MN.6: 2 residues within 4Å: Chain A: E.89 Chain C: A.1 No protein-ligand interaction detected (PLIP)

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

NA.3: 5 residues within 4Å: Chain A: S.222, S.229, I.233, G.234 Chain B: A.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.222, A:S.229

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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