SMTL ID : 2alz.1

Ternary Complex of hPoli with DNA and dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

DT-DG-DG-DG-DG-DT-DC-DC-DT.1: 32 residues within 4Å: Chain A: Q.35, K.36, Y.37, L.38, V.40, L.54, E.73, L.75, R.79, F.101, P.275, Q.276, S.277, F.278, S.279, E.280, E.281, S.283, K.285, R.307 Chain B: Q.337, P.339 Ligands: DA-DG-DG-DA-DC-DC-DOC.2, DA-DG-DG-DA-DC-DC-DOC.2, DA-DG-DG-DA-DC-DC-DOC.2, DA-DG-DG-DA-DC-DC-DOC.2, DA-DG-DG-DA-DC-DC-DOC.2, DA-DG-DG-DA-DC-DC-DOC.2, DA-DG-DG-DA-DC-DC-DOC.2, DCP.5, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DA-DG-DG-DA-DC-DC-DOC.7 Protein-ligand interaction information (PLIP) not available DT-DG-DG-DG-DG-DT-DC-DC-DT.6: 32 residues within 4Å: Chain A: Q.337, P.339 Chain B: Q.35, K.36, Y.37, L.38, V.40, L.54, E.73, L.75, R.79, F.101, P.275, Q.276, S.277, F.278, S.279, E.280, E.281, S.283, K.285, R.307 Ligands: DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DA-DG-DG-DA-DC-DC-DOC.2, DA-DG-DG-DA-DC-DC-DOC.7, DA-DG-DG-DA-DC-DC-DOC.7, DA-DG-DG-DA-DC-DC-DOC.7, DA-DG-DG-DA-DC-DC-DOC.7, DA-DG-DG-DA-DC-DC-DOC.7, DA-DG-DG-DA-DC-DC-DOC.7, DA-DG-DG-DA-DC-DC-DOC.7, DCP.10 Protein-ligand interaction information (PLIP) not available

2 x DA- DG- DG- DA- DC- DC- DOC: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'(Non-covalent)

DA-DG-DG-DA-DC-DC-DOC.2: 26 residues within 4Å: Chain A: L.99, G.100, E.103, K.183, P.216, G.217, I.218, G.219, Y.220, K.221, T.222, E.334, S.335, R.336 Ligands: DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DT-DG-DG-DG-DG-DT-DC-DC-DT.1, MG.3, DCP.5, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DA-DG-DG-DA-DC-DC-DOC.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.183 DA-DG-DG-DA-DC-DC-DOC.7: 26 residues within 4Å: Chain B: L.99, G.100, E.103, K.183, P.216, G.217, I.218, G.219, Y.220, K.221, T.222, E.334, S.335, R.336 Ligands: DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DA-DG-DG-DA-DC-DC-DOC.2, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, MG.8, DCP.10 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.183

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.10, D.102, E.103 Ligands: DA-DG-DG-DA-DC-DC-DOC.2, MG.4, DCP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.10, A:E.103 MG.4: 5 residues within 4Å: Chain A: D.10, L.11, D.102 Ligands: MG.3, DCP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.10, A:L.11, A:D.102 MG.8: 6 residues within 4Å: Chain B: D.10, D.102, E.103 Ligands: DA-DG-DG-DA-DC-DC-DOC.7, MG.9, DCP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.10, B:E.103 MG.9: 5 residues within 4Å: Chain B: D.10, L.11, D.102 Ligands: MG.8, DCP.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.10, B:L.11, B:D.102

2 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.5: 18 residues within 4Å: Chain A: D.10, L.11, D.12, C.13, F.14, Y.15, V.40, T.41, Y.44, R.47, K.53, D.102, K.190 Ligands: DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DT-DG-DG-DG-DG-DT-DC-DC-DT.1, DA-DG-DG-DA-DC-DC-DOC.2, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.15 Hydrogen bonds: A:L.11, A:C.13, A:F.14, A:Y.15, A:T.41 Water bridges: A:F.101, A:K.190 Salt bridges: A:R.47, A:R.47, A:K.53, A:K.53, A:K.53, A:K.190 DCP.10: 18 residues within 4Å: Chain B: D.10, L.11, D.12, C.13, F.14, Y.15, V.40, T.41, Y.44, R.47, K.53, D.102, K.190 Ligands: DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DT-DG-DG-DG-DG-DT-DC-DC-DT.6, DA-DG-DG-DA-DC-DC-DOC.7, MG.8, MG.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.15 Hydrogen bonds: B:L.11, B:C.13, B:F.14, B:Y.15, B:T.41, B:T.41, B:Y.44 Water bridges: B:Y.15, B:F.101, B:K.190 Salt bridges: B:R.47, B:R.47, B:K.53, B:K.53, B:K.53, B:K.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nair, D.T. et al., Human DNA Polymerase iota Incorporates dCTP Opposite Template G via a G.C+ Hoogsteen Base Pair. Structure (2005)

Release Date

2005-10-25

Peptides

DNA polymerase iota: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA polymerase iota

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