SMTL ID : 4jrp.2 (2 other biounits)

Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain B: R.151, R.206 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.151, B:R.206 SO4.2: 4 residues within 4Å: Chain B: Y.210, T.213, H.214, K.219 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.213 Salt bridges: B:H.214, B:K.219 SO4.3: 4 residues within 4Å: Chain B: H.25, P.26, A.27, L.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.25, B:A.27, B:L.28 Salt bridges: B:H.25 SO4.4: 5 residues within 4Å: Chain B: N.417, F.418, P.419, G.420, T.421 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.420 SO4.5: 5 residues within 4Å: Chain B: N.160, S.166, F.167, R.168, H.171 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.160, B:N.160, B:F.167, B:R.168 Salt bridges: B:R.168 SO4.6: 3 residues within 4Å: Chain B: P.231, L.337, R.341 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.341 SO4.7: 3 residues within 4Å: Chain B: F.375, S.376, D.377 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.377 Water bridges: B:S.376, B:A.378 SO4.8: 1 residues within 4Å: Chain B: R.203 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.203 SO4.9: 3 residues within 4Å: Chain A: X.1 Chain B: Q.132, K.384 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.132 Water bridges: B:K.384 Salt bridges: B:K.384

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.10: 3 residues within 4Å: Chain B: F.442, G.445, Y.446 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korada, S.K. et al., Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion. Nucleic Acids Res. (2013)

Release Date

2013-05-08

Peptides

Exodeoxyribonuclease I: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

Exodeoxyribonuclease I

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