SMTL ID : 3slp.1

Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: D.122, E.132 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.122, H2O.4 CA.3: 3 residues within 4Å: Chain B: D.122, E.132, L.133 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.122, B:E.132, B:L.133, H2O.6, H2O.9 CA.6: 3 residues within 4Å: Chain C: S.120, D.122, E.132 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.122, H2O.16, H2O.16, H2O.17

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: R.31, T.36, A.37, S.38, C.119, S.120 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.37, A:S.38, A:A.118, A:S.120 Water bridges: A:S.120, A:Q.160, A:Q.160, A:Q.160, A:S.164 Salt bridges: A:R.31 PO4.5: 8 residues within 4Å: Chain B: R.31, T.36, A.37, S.38, A.118, C.119, S.120, Q.160 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.36, B:T.36, B:A.37, B:S.38, B:S.120, B:S.120, B:Q.160 Water bridges: B:Q.22, B:R.31, B:S.120, B:S.120, B:S.164 Salt bridges: B:R.31 PO4.8: 6 residues within 4Å: Chain C: R.31, T.36, A.37, S.38, C.119, S.120 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.36, C:A.37, C:S.38, C:S.120 Water bridges: C:Q.160, C:Q.160 Salt bridges: C:R.31

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain B: A.80 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: R.111, R.169 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-07-20

Peptides

Exonuclease: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Exonuclease

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