SMTL ID : 3h4d.1

Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DA- DG- DG- DA- DC- DC- DOC: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))(Non-covalent)

DA-DG-DG-DA-DC-DC-DOC.1: 22 residues within 4Å: Chain A: L.99, G.100, D.102, E.103, K.183, G.217, I.218, G.219, K.221, T.222, E.334, S.335, R.336 Ligands: DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, MG.4, DGT.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.183

1 x DT- BRU- DG- DG- DG- DT- DC- DC- DT: 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T)(Non-covalent)

DT-BRU-DG-DG-DG-DT-DC-DC-DT.2: 25 residues within 4Å: Chain A: Q.35, K.36, Y.37, L.38, V.40, E.73, L.75, P.275, Q.276, S.277, F.278, S.279, E.280, E.281, S.283, R.307, R.323 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DGT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.283 Salt bridges: A:R.323

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.10, L.11, D.102 Ligands: MG.4, DGT.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.10, A:L.11 MG.4: 6 residues within 4Å: Chain A: D.10, D.102, E.103 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, MG.3, DGT.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.103

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.5: 20 residues within 4Å: Chain A: D.10, L.11, D.12, C.13, F.14, Y.15, Q.35, V.40, T.41, Y.44, R.47, K.53, L.54, D.102, K.190 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, DT-BRU-DG-DG-DG-DT-DC-DC-DT.2, MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.41 Hydrogen bonds: A:C.13, A:F.14, A:Y.15, A:Q.35, A:T.41, A:D.102 Water bridges: A:Q.35, A:K.190, A:K.190, A:K.190, A:K.190 Salt bridges: A:R.47, A:R.47, A:K.53, A:K.53, A:K.53, A:K.190 pi-Stacking: A:Y.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jain, R. et al., Replication across template T/U by human DNA polymerase-iota. Structure (2009)

Release Date

2009-07-21

Peptides

DNA polymerase iota: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase iota

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