SMTL ID : 5kt6.1

Teranry complex of human DNA polymerase iota(1-445) inserting dCMPNPP opposite template G in the presence of Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.54 Å

Oligo State

monomer

Ligands

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

DT-DG-DG-DG-DG-DT-DC-DC-DT.1: 29 residues within 4Å: Chain A: Q.84, K.85, Y.86, L.87, V.89, E.122, L.124, R.128, P.324, Q.325, S.326, F.327, S.328, E.329, E.330, S.332, F.333, K.334, R.356, R.372, T.429 Ligands: DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, 0KX.3 Protein-ligand interaction information (PLIP) not available

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

DA-DG-DG-DA-DC-DC-DC.2: 26 residues within 4Å: Chain A: L.148, G.149, D.151, E.152, K.232, I.264, P.265, G.266, I.267, G.268, Y.269, K.270, T.271, E.383, S.384, R.385, Q.386 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, 0KX.3, MG.5 Protein-ligand interaction information (PLIP) not available

1 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.3: 18 residues within 4Å: Chain A: D.59, L.60, D.61, C.62, F.63, Y.64, V.89, T.90, Y.93, R.96, K.102, D.151, K.239 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-DC.2, MG.4, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.64 Hydrogen bonds: A:D.59, A:C.62, A:F.63, A:Y.64, A:Y.93 Salt bridges: A:R.96, A:K.102, A:K.239

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.59, L.60, D.151 Ligands: 0KX.3, MG.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.59, A:L.60, A:D.151 MG.5: 6 residues within 4Å: Chain A: D.59, D.151, E.152 Ligands: DA-DG-DG-DA-DC-DC-DC.2, 0KX.3, MG.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.59, A:D.59, A:D.151, A:D.151, A:E.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, J.Y. et al., Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota. J.Biol.Chem. (2016)

Release Date

2016-08-31

Peptides

DNA polymerase iota: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase iota

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