SMTL ID : 5dkw.1 (1 other biounit)

Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

monomer

Ligands

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

DG-DC-DC-DG.1: 20 residues within 4Å: Chain A: Y.19, W.26, R.27, G.30, Y.31, I.54, P.55, G.56, I.57, G.58, K.59, R.60, M.61, K.64, K.76 Chain B: C.1, G.2, G.3, C.4 Ligands: CA.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.26 Hydrogen bonds: A:W.26 Water bridges: A:R.269 Salt bridges: A:R.269, A:K.273 pi-Stacking: A:W.26 pi-Cation interactions: A:R.269, A:R.269

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.2: 20 residues within 4Å: Chain A: I.93, W.94, G.95, A.96, G.97, T.98, K.99, T.100, K.224, R.240, Y.257, F.258 Chain B: G.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: DTP.3 Protein-ligand interaction information (PLIP) not available

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.3: 16 residues within 4Å: Chain A: R.138, G.168, S.169, R.172, G.178, D.179, D.181, Y.257, F.258, T.259, G.260, A.262, N.265 Chain B: G.5 Ligands: DC-DA-DG-DT-DA-DC.2, CA.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.169, A:S.169, A:G.178, A:D.179 Water bridges: A:Y.170, A:R.172, A:R.172, A:A.262, A:R.269, A:R.269 Salt bridges: A:R.138, A:R.172

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: D.179, D.181 Ligands: DTP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.179, H2O.2, H2O.2 CA.5: 4 residues within 4Å: Chain A: C.52, I.54, I.57 Ligands: DG-DC-DC-DG.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.52, A:I.54, A:I.57, H2O.4, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, M.S. et al., Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda. J.Am.Chem.Soc. (2016)

Release Date

2016-02-24

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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