SMTL ID : 5cwr.2 (1 other biounit)

Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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: 24 residues within 4Å: Chain A: I.92, W.93, G.94, A.95, G.96, T.97, K.98, T.99, D.180, K.223, L.225, R.239, D.241, Y.256, F.257 Chain B: G.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: DCP.3, CA.4 Protein-ligand interaction information (PLIP) not available

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.18, W.25, R.26, G.29, Y.30, I.53, P.54, G.55, I.56, G.57, K.58, R.59, M.60, K.63, K.75 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.3: 18 residues within 4Å: Chain A: R.137, G.167, S.168, R.171, C.176, G.177, D.178, D.180, Y.256, F.257, T.258, G.259, A.261, N.264 Chain B: G.5 Ligands: DC-DA-DG-DT-DA-DC.1, CA.4, CA.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.261 Hydrogen bonds: A:S.168, A:S.168, A:R.171, A:G.177, A:D.178, A:D.178, A:N.264 Water bridges: A:Y.169, A:Y.169, A:D.178, A:D.178, A:A.261 Salt bridges: A:R.137, A:R.171

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.178, D.180, D.241 Ligands: DC-DA-DG-DT-DA-DC.1, DCP.3, CA.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.178, A:D.180, A:D.241 CA.5: 4 residues within 4Å: Chain A: D.178, D.180 Ligands: DCP.3, CA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:D.178, A:D.180, H2O.1

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
B

DNA polymerase lambda

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