SMTL ID : 3c5f.2 (1 other biounit)

Structure of a binary complex of the R517A Pol lambda mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- DC: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')(Non-covalent)

DC-DA-DG-DT-DA-DC.1: 22 residues within 4Å: Chain A: G.6, T.7, A.8, C.9, T.10, G.11 Chain B: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, D.189, K.232, L.234, R.248, D.250, Y.265, F.266 Ligands: NA.3 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')(Non-covalent)

DG-DC-DC-DG.2: 19 residues within 4Å: Chain A: C.1, G.2, G.3, C.4 Chain B: Y.27, W.34, R.35, Y.39, I.62, P.63, G.64, I.65, G.66, K.67, R.68, M.69, K.72, K.84 Ligands: NA.5 Protein-ligand interaction information (PLIP) not available

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

NA.3: 5 residues within 4Å: Chain B: S.99, I.101, G.103, A.104 Ligands: DC-DA-DG-DT-DA-DC.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.101, B:G.103, B:A.104 NA.4: 4 residues within 4Å: Chain B: S.257, E.258, H.290, A.291 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.290 Water bridges: B:T.313, B:T.313 NA.5: 4 residues within 4Å: Chain B: C.60, I.62, I.65 Ligands: DG-DC-DC-DG.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.60, B:I.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bebenek, K. et al., Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. Embo Rep. (2008)

Release Date

2008-09-02

Peptides

DNA polymerase lambda: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

DNA polymerase lambda

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