SMTL ID : 2bcr.1

DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

DG-DC-DC-DG.1: 18 residues within 4Å: Chain A: C.1, G.2, G.3, C.4 Chain B: W.34, R.35, G.38, Y.39, I.62, P.63, G.64, I.65, G.66, K.67, R.68, M.69, K.72 Ligands: NA.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.34, B:W.34, B:L.37 Hydrogen bonds: B:R.277 Water bridges: B:W.34, B:K.41, B:K.281, B:K.281, B:K.281 Salt bridges: B:R.274, B:K.281, B:K.281, B:H.301 pi-Stacking: B:W.34

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

DC-DA-DG-DT-DA-DC-DG.2: 34 residues within 4Å: Chain A: C.5, G.6, T.8, A.9, C.10, T.11, G.12 Chain B: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, G.176, R.180, D.187, D.189, L.234, R.248, D.250, Y.265, F.266, T.267, G.268, S.269, A.270, N.273, R.277 Ligands: EDO.3, MG.4, NA.6, PPV.8 Protein-ligand interaction information (PLIP) not available

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

EDO.3: 3 residues within 4Å: Chain B: T.108, M.111 Ligands: DC-DA-DG-DT-DA-DC-DG.2 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain B: R.212, L.217, T.218, D.219, D.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.212, B:D.220 EDO.10: 5 residues within 4Å: Chain A: A.9 Chain B: Q.231, V.254, E.258, H.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.258 Water bridges: B:K.232 EDO.11: 5 residues within 4Å: Chain B: R.179, T.315, E.316, K.317, Y.327 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.179, B:T.315, B:E.316, B:E.316, B:K.317 EDO.12: 5 residues within 4Å: Chain B: R.238, G.241, P.242, G.243, R.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.244, B:R.244

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: D.187, D.189 Ligands: DC-DA-DG-DT-DA-DC-DG.2, PPV.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.189, H2O.7

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

NA.5: 2 residues within 4Å: Chain A: T.11 Chain B: S.223 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.223 NA.6: 6 residues within 4Å: Chain B: S.99, I.101, W.102, G.103, A.104 Ligands: DC-DA-DG-DT-DA-DC-DG.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.101, B:G.103, B:A.104 NA.7: 5 residues within 4Å: Chain B: C.60, I.62, P.63, I.65 Ligands: DG-DC-DC-DG.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.65, B:I.65

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.8: 9 residues within 4Å: Chain B: R.146, G.176, S.177, R.180, G.186, D.187, D.189 Ligands: DC-DA-DG-DT-DA-DC-DG.2, MG.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.177, B:S.177, B:G.186, B:D.187 Water bridges: B:Y.178, B:Y.178, B:R.248, B:R.248 Salt bridges: B:R.146, B:R.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Diaz, M. et al., Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase. Cell(Cambridge,Mass.) (2006)

Release Date

2006-03-07

Peptides

DNA polymerase lambda: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA polymerase lambda

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