SMTL ID : 3uq2.1

Crystal structure of the post-catalytic product complex of polymerase lambda with an rCMP inserted opposite a templating G and dAMP inserted opposite a templating T at the primer terminus.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-C-DA.1: 31 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, G.175, R.179, D.186, D.188, L.228, R.242, D.244, Y.259, F.260, T.261, G.262, A.264, N.267 Chain B: T.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: PPV.3, MG.4, NA.5 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: 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, I.61, 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 Protein-ligand interaction information (PLIP) not available

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3: 10 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, C.184, G.185, D.186, D.188 Ligands: DC-DA-DG-DT-DA-C-DA.1, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:G.185, A:D.186 Water bridges: A:R.179, A:K.181, A:D.186, A:R.242 Salt bridges: A:R.145, A:R.179

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.186, D.188 Ligands: DC-DA-DG-DT-DA-C-DA.1, PPV.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.2

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

NA.5: 6 residues within 4Å: Chain A: S.98, I.100, W.101, G.102, A.103 Ligands: DC-DA-DG-DT-DA-C-DA.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.98, A:G.102, A:A.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gosavi, R.A. et al., The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda. Nucleic Acids Res. (2012)

Release Date

2012-05-23

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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