SMTL ID : 2bcv.1

DNA polymerase lambda in complex with Dttp and a DNA duplex containing an unpaired Dtmp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.34, B:L.37 Hydrogen bonds: B:W.34, B:R.277, B:R.298 Water bridges: B:K.33, B:R.274, 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, B:W.34

1 x DC- DA- DG- DT- DA- O2C: 5'-D(*CP*AP*GP*TP*AP*(O2C))-3'(Non-covalent)

DC-DA-DG-DT-DA-O2C.2: 24 residues within 4Å: Chain A: A.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, K.232, L.234, R.248, D.250, Y.265, F.266 Ligands: NA.4, NA.6, TTP.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.232, B:R.248, B:Y.265

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain B: D.187, D.189 Ligands: NA.6, TTP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.189, H2O.10

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

NA.4: 5 residues within 4Å: Chain B: S.99, I.101, G.103, A.104 Ligands: DC-DA-DG-DT-DA-O2C.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.103, B:A.104, B:A.104 NA.5: 2 residues within 4Å: Chain A: T.11 Chain B: S.223 5 PLIP interactions: 5 interactions with chain B Water bridges: B:S.223, B:S.223, B:S.223, B:E.225, B:E.226 NA.6: 6 residues within 4Å: Chain B: D.187, D.189, D.250 Ligands: DC-DA-DG-DT-DA-O2C.2, MG.3, TTP.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.189, B:D.250 Water bridges: B:R.248

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.7: 19 residues within 4Å: Chain A: A.5 Chain B: R.146, G.176, S.177, R.180, C.185, G.186, D.187, D.189, Y.265, F.266, T.267, G.268, S.269, A.270, N.273 Ligands: DC-DA-DG-DT-DA-O2C.2, MG.3, NA.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:A.270 Hydrogen bonds: B:S.177, B:S.177, B:R.180, B:G.186, B:D.187, B:N.273 Water bridges: B:R.146, B:S.177, B:R.180, B:R.180, B:R.180, B:D.189, B:R.248, B:R.248, B:A.270 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

Related Entries With Identical Sequence