SMTL ID : 2fll.1

Ternary complex of human DNA polymerase iota with DNA and dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x DA- DG- DG- DA- DC- DC- DOC: DNA primer strand(Non-covalent)

DA-DG-DG-DA-DC-DC-DOC.1: 27 residues within 4Å: Chain A: A.4, G.5, G.6, G.7, T.8, C.9, C.10, T.11 Chain B: L.123, G.124, E.127, K.207, I.239, P.240, G.241, I.242, G.243, Y.244, K.245, T.246, E.358, S.359, R.360 Chain C: T.11 Ligands: MG.3, TTP.4, DA-DG-DG-DA-DC-DC-DOC.5 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.127 Salt bridges: B:K.207 DA-DG-DG-DA-DC-DC-DOC.5: 27 residues within 4Å: Chain A: T.11 Chain C: A.4, G.5, G.6, G.7, T.8, C.9, C.10, T.11 Chain D: L.123, G.124, E.127, K.207, I.239, P.240, G.241, I.242, G.243, Y.244, K.245, T.246, E.358, S.359, R.360 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, MG.7, TTP.8 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.207

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: D.34, L.35, D.126 Ligands: MG.3, TTP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.34, B:L.35, B:D.126 MG.3: 6 residues within 4Å: Chain B: D.34, D.126, E.127 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, MG.2, TTP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.34, B:E.127 MG.6: 5 residues within 4Å: Chain D: D.34, L.35, D.126 Ligands: MG.7, TTP.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.34, D:L.35, D:D.126 MG.7: 6 residues within 4Å: Chain D: D.34, D.126, E.127 Ligands: DA-DG-DG-DA-DC-DC-DOC.5, MG.6, TTP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.34, D:E.127

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

TTP.4: 18 residues within 4Å: Chain A: A.4, G.5 Chain B: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, D.126, K.214 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, MG.2, MG.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.39 Hydrogen bonds: B:L.35, B:C.37, B:F.38, B:Y.39 Water bridges: B:D.34, B:K.214 Salt bridges: B:R.71, B:R.71, B:K.77, B:K.77, B:K.77, B:K.214 TTP.8: 18 residues within 4Å: Chain C: A.4, G.5 Chain D: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, D.126, K.214 Ligands: DA-DG-DG-DA-DC-DC-DOC.5, MG.6, MG.7 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:Y.39 Hydrogen bonds: D:L.35, D:C.37, D:F.38, D:Y.39, D:Y.39, D:T.65, D:Y.68 Water bridges: D:D.34, D:K.214 Salt bridges: D:R.71, D:R.71, D:K.77, D:K.77, D:K.77, D:K.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nair, D.T. et al., An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site. Structure (2006)

Release Date

2006-12-12

Peptides

DNA polymerase iota: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

D
A

DNA polymerase iota

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