SMTL ID : 5kt3.1

Teranry complex of human DNA polymerase iota(26-445) inserting dCMPNPP opposite template G in the presence of Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 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.126, 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, Q.361 Ligands: 0KX.2, MN.4, MN.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.2: 19 residues within 4Å: Chain A: G.3, G.4 Chain B: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, L.78, D.126, K.214 Ligands: DA-DG-DG-DA-DC-DC-DC.1, MN.3, MN.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.39 Hydrogen bonds: B:C.37, B:F.38, B:Y.39, B:T.65, B:Y.68, B:R.71 Water bridges: B:Q.59 Salt bridges: B:R.71, B:K.77, B:K.214

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

MN.3: 5 residues within 4Å: Chain B: D.34, L.35, D.126 Ligands: 0KX.2, MN.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.34, B:L.35, B:D.126 MN.4: 6 residues within 4Å: Chain B: D.34, D.126, E.127 Ligands: DA-DG-DG-DA-DC-DC-DC.1, 0KX.2, MN.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.34, B:D.126, B:E.127 MN.5: 4 residues within 4Å: Chain B: K.237, I.239, I.242 Ligands: DA-DG-DG-DA-DC-DC-DC.1 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:K.237, B:I.239, B:I.242

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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