SMTL ID : 3hw8.1

ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a C in the scrunch site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- DT: 5'-D(*CP*AP*GP*TP*AP*T)-3'(Non-covalent)

DC-DA-DG-DT-DA-DT.1: 21 residues within 4Å: Chain A: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, L.234, R.248, D.250, Y.265 Chain B: A.6, A.7, T.8, A.9, C.10, T.11, G.12 Ligands: NA.5, D3T.8 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.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.7 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.8 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.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.250 Water bridges: A:R.248 NA.5: 6 residues within 4Å: Chain A: S.99, I.101, W.102, G.103, A.104 Ligands: DC-DA-DG-DT-DA-DT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.101, A:G.103, A:A.104 NA.6: 2 residues within 4Å: Chain A: S.223 Chain B: T.11 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.223, A:E.225, A:E.226 NA.7: 6 residues within 4Å: Chain A: C.60, S.61, I.62, P.63, I.65 Ligands: DG-DC-DC-DG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.64, A:I.65, A:I.65

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

D3T.8: 19 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, R.274 Chain B: A.6 Ligands: DC-DA-DG-DT-DA-DT.1, MG.3, NA.4 11 PLIP interactions: 11 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, A:R.274 Water bridges: A:R.180 Salt bridges: A:R.146, A:R.180

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

EDO.9: 1 residues within 4Å: Chain A: R.245 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.141, A:R.245, A:R.245, A:R.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Diaz, M. et al., Scrunching Durning DNA Repair Synthesis. To be Published

Release Date

2009-08-25

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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