SMTL ID : 3sz4.1

Crystal Structure of LHK-Exo in complex with dAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.102, E.112, I.113 Ligands: D5M.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.102, A:E.112, A:I.113 MG.3: 4 residues within 4Å: Chain B: D.102, E.112, I.113 Ligands: D5M.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.102, B:E.112, B:I.113 MG.5: 4 residues within 4Å: Chain C: D.102, E.112, I.113 Ligands: D5M.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.102, C:E.112, C:I.113

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

D5M.2: 9 residues within 4Å: Chain A: F.9, R.12, T.17, A.18, S.19, A.99, S.100, Q.137 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.12, A:T.17, A:A.18, A:S.19, A:S.19, A:S.100, A:Q.137 Water bridges: A:E.112 Salt bridges: A:R.12 pi-Stacking: A:W.8 D5M.4: 9 residues within 4Å: Chain B: F.9, R.12, T.17, A.18, S.19, A.99, S.100, Q.137 Ligands: MG.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.12, B:T.17, B:A.18, B:S.19, B:S.19, B:S.100, B:Q.137 Water bridges: B:E.112 Salt bridges: B:R.12 pi-Stacking: B:W.8 D5M.6: 9 residues within 4Å: Chain C: F.9, R.12, T.17, A.18, S.19, A.99, S.100, Q.137 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.12, C:T.17, C:A.18, C:S.19, C:S.19, C:S.100, C:Q.137 Water bridges: C:E.112 Salt bridges: C:R.12 pi-Stacking: C:W.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, W. et al., Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis. Nucleic Acids Res. (2011)

Release Date

2012-02-15

Peptides

Exonuclease: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Exonuclease

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