SMTL ID : 5kt7.1

Teranry complex of human DNA polymerase iota(1-445) inserting dCMPNPP opposite template G in the presence of Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

monomer

Ligands

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.1: 26 residues within 4Å: Chain A: G.3, G.4, G.5, G.6, T.7, C.8, C.9, T.10 Chain B: D.59, 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: MN.2, 0KX.3 Protein-ligand interaction information (PLIP) not available

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain B: D.59, D.151, E.152 Ligands: DA-DG-DG-DA-DC-DC-DC.1, 0KX.3, MN.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.59, B:D.151, B:D.151, B:E.152 MN.4: 5 residues within 4Å: Chain B: D.59, L.60, D.151 Ligands: MN.2, 0KX.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.59, B:L.60, B:D.151

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

0KX.3: 20 residues within 4Å: Chain A: G.3, G.4 Chain B: D.59, L.60, D.61, C.62, F.63, Y.64, Q.84, V.89, T.90, Y.93, R.96, K.102, L.103, D.151, K.239 Ligands: DA-DG-DG-DA-DC-DC-DC.1, MN.2, MN.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.64 Hydrogen bonds: B:C.62, B:F.63, B:Y.64, B:R.96 Salt bridges: B:R.96, B:K.102, B:K.239

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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA polymerase iota

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