SMTL ID : 4x5v.1

Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

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

DG-DC-DC-DG.1: 17 residues within 4Å: Chain A: Y.17, W.24, R.25, G.28, Y.29, P.53, G.54, I.55, G.56, K.57, R.58, M.59, K.62 Chain B: C.1, G.2, G.3, C.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.24 Hydrogen bonds: A:W.24, A:R.267 Salt bridges: A:R.264, A:K.271, A:K.271, A:R.288, A:H.291 pi-Stacking: A:W.24, A:W.24

1 x DC- DA- DG- DT- DA- DC- 8OG: DNA (5'-D(*CP*AP*GP*TP*AP*CP*(8OG))-3')(Non-covalent)

DC-DA-DG-DT-DA-DC-8OG.2: 31 residues within 4Å: Chain A: I.91, W.92, G.93, A.94, G.95, T.96, K.97, T.98, G.166, R.170, D.177, D.179, L.224, R.238, D.240, Y.255, F.256, T.257, G.258, A.260, N.263 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.3, MG.4, CIT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.170, A:N.263 Water bridges: A:D.177

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

NA.3: 4 residues within 4Å: Chain A: D.177, D.179 Ligands: DC-DA-DG-DT-DA-DC-8OG.2, CIT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.177 Water bridges: A:S.167

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: S.89, I.91, W.92, G.93, A.94 Ligands: DC-DA-DG-DT-DA-DC-8OG.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.89, A:I.91, A:A.94, H2O.5, H2O.6

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 11 residues within 4Å: Chain A: R.136, G.166, S.167, R.170, C.175, G.176, D.177, D.179, R.238 Ligands: DC-DA-DG-DT-DA-DC-8OG.2, NA.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.167, A:S.167, A:G.176, A:D.177, A:D.177, A:D.177 Water bridges: A:R.136, A:S.167, A:R.170, A:R.170, A:D.177, A:R.238, A:R.238, A:R.238, A:R.238 Salt bridges: A:R.136, A:R.136, A:R.170, A:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burak, M.J. et al., Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda. Nucleic Acids Res. (2015)

Release Date

2015-10-28

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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