SMTL ID : 3uq1.1

Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and a rCMP at the primer terminus.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-C.1: 24 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, D.188, L.228, R.242, D.244, Y.259, F.260 Chain B: T.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: MN.8, NA.9, F2A.10 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:W.33, A:L.36 Hydrogen bonds: A:K.222, A:K.222, A:T.225, A:K.226, A:Y.259, A:Y.259, A:R.271, A:S.282 Water bridges: A:T.130, A:T.130, A:T.130, A:Q.131, A:E.224, A:E.224, A:K.275, A:K.275, A:K.275, A:R.292, A:R.292, A:H.295 Salt bridges: A:R.268, A:K.275, A:K.275, A:H.284, A:R.292, A:H.295, A:K.298 pi-Stacking: A:W.33, A:W.33

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 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.6 Protein-ligand interaction information (PLIP) not available

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

DT-DA-DC-DT-DG.3: 11 residues within 4Å: Chain A: L.170, V.172, Y.250, F.253, P.308, T.309 Ligands: DC-DA-DG-DT-DA.4, DC-DA-DG-DT-DA.4, DC-DA-DG-DT-DA.4, DC-DA-DG-DT-DA.4, DC-DA-DG-DT-DA.4 Protein-ligand interaction information (PLIP) not available

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

DC-DA-DG-DT-DA.4: 10 residues within 4Å: Chain A: Q.159, Q.163, L.169, L.170, C.171 Ligands: DT-DA-DC-DT-DG.3, DT-DA-DC-DT-DG.3, DT-DA-DC-DT-DG.3, DT-DA-DC-DT-DG.3, DT-DA-DC-DT-DG.3 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.186, D.188 Ligands: MN.8, F2A.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.132

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

NA.6: 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 NA.9: 6 residues within 4Å: Chain A: S.98, I.100, W.101, G.102, A.103 Ligands: DC-DA-DG-DT-DA-C.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.102, A:A.103, A:A.103

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: R.271, E.283 Chain B: G.6, T.7 Ligand excluded by PLIP

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 6 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-C.1, MG.5, F2A.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, A:D.244, H2O.119

1 x F2A: 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE(Non-covalent)

F2A.10: 20 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, C.184, G.185, D.186, D.188, Y.259, F.260, T.261, G.262, S.263, A.264, N.267 Chain B: T.5, G.6 Ligands: DC-DA-DG-DT-DA-C.1, MG.5, MN.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:R.179, A:R.179, A:G.185, A:D.186, A:N.267 Water bridges: A:D.186, A:A.264, A:R.268 Salt bridges: A:R.145

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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