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

Binary complex of a DNA polymerase lambda loop mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- DC: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')(Non-covalent)

DC-DA-DG-DT-DA-DC.1: 21 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, R.242, D.244, Y.259, F.260 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.3, NA.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.33 Hydrogen bonds: A:W.33, A:K.40, A:T.130, A:T.130, A:K.222, A:E.224, A:Y.259, A:Y.259 Water bridges: A:T.225, A:K.226, A:K.226, A:Y.259, A:R.268, A:R.271, A:R.271, A:R.271, A:R.271, A:K.275 Salt bridges: A:R.271, A:K.275 pi-Stacking: A:W.33 pi-Cation interactions: A:R.271, A:R.271

1 x DG- DC- DC- DG: DNA (5'-D(P*GP*CP*CP*G)-3')(Non-covalent)

DG-DC-DC-DG.2: 19 residues within 4Å: Chain A: Y.26, W.33, R.34, G.37, Y.38, P.62, G.63, I.64, G.65, K.66, R.67, M.68, K.71, K.83 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.5 Protein-ligand interaction information (PLIP) not available

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

NA.3: 4 residues within 4Å: Chain A: S.98, I.100, A.103 Ligands: DC-DA-DG-DT-DA-DC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.100, A:A.103 NA.4: 4 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.244 NA.5: 5 residues within 4Å: Chain A: C.59, I.61, P.62, I.64 Ligands: DG-DC-DC-DG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.61, A:I.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bebenek, K. et al., Loop 1 modulates the fidelity of DNA polymerase lambda. Nucleic Acids Res. (2010)

Release Date

2010-05-19

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

DNA polymerase lambda

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