SMTL ID : 3c5g.1 (1 other biounit)

Structure of a ternary complex of the R517K Pol lambda mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- 2DT: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3')(Non-covalent)

DC-DA-DG-DT-DA-2DT.1: 21 residues within 4Å: Chain A: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, R.248, D.250, Y.265 Chain B: A.5, A.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.5, D3T.7, NA.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.265 Water bridges: A:K.232, A:K.232 Salt bridges: A:R.248

1 x DG- DC- DC- DG: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')(Non-covalent)

DG-DC-DC-DG.2: 20 residues within 4Å: Chain A: Y.27, W.34, R.35, G.38, Y.39, P.63, G.64, I.65, G.66, K.67, R.68, M.69, K.72, K.84 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.6, EDO.8 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.187, D.189 Ligands: NA.4, D3T.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, A:D.189, H2O.7

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

NA.4: 5 residues within 4Å: Chain A: D.187, D.189, D.250 Ligands: MG.3, D3T.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.250 NA.5: 6 residues within 4Å: Chain A: S.99, I.101, W.102, G.103, A.104 Ligands: DC-DA-DG-DT-DA-2DT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.99, A:G.103, A:A.104 NA.6: 6 residues within 4Å: Chain A: C.60, I.62, P.63, G.64, I.65 Ligands: DG-DC-DC-DG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.60, A:G.64, A:I.65 NA.9: 3 residues within 4Å: Chain A: Q.132 Ligands: DC-DA-DG-DT-DA-2DT.1, DC-DA-DG-DT-DA-2DT.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.132 Water bridges: A:Q.132, A:Q.132, A:Q.133

1 x D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

D3T.7: 18 residues within 4Å: Chain A: R.146, G.176, S.177, R.180, C.185, G.186, D.187, D.189, Y.265, F.266, G.268, S.269, A.270, N.273 Chain B: A.5 Ligands: DC-DA-DG-DT-DA-2DT.1, MG.3, NA.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.270 Hydrogen bonds: A:S.177, A:S.177, A:S.177, A:G.186, A:D.187, A:N.273 Water bridges: A:R.146, A:R.180, A:R.180, A:R.180 Salt bridges: A:R.146, A:R.180

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain B: G.2, G.3, C.4 Ligands: DG-DC-DC-DG.2, DG-DC-DC-DG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bebenek, K. et al., Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. Embo Rep. (2008)

Release Date

2008-07-29

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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