SMTL ID : 3epg.1

Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

DCP.1: 16 residues within 4Å: Chain A: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, D.126, K.214 Chain B: C.18 Chain C: G.4, G.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.39 Hydrogen bonds: A:C.37, A:F.38, A:Y.39, A:T.65, A:D.126 Salt bridges: A:R.71, A:R.71, A:K.77, A:K.77, A:K.77, A:K.214 DCP.6: 16 residues within 4Å: Chain D: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, D.126, K.214 Chain E: C.18 Chain F: G.4, G.5 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:Y.39 Hydrogen bonds: D:C.37, D:F.38, D:Y.39, D:Y.39, D:T.65, D:T.65, D:Y.68, D:D.126, D:D.126 Salt bridges: D:R.71, D:R.71, D:K.77, D:K.77, D:K.77, D:K.214

8 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: K.237, E.238, I.239, P.240, I.242 Chain B: C.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.239, A:G.241 NA.3: 1 residues within 4Å: Chain A: E.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.115 NA.4: 1 residues within 4Å: Chain A: P.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.240 NA.5: 1 residues within 4Å: Chain C: C.9 No protein-ligand interaction detected (PLIP) NA.7: 6 residues within 4Å: Chain D: K.237, E.238, I.239, P.240, I.242 Chain E: C.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.241, D:I.242 NA.8: 1 residues within 4Å: Chain D: E.115 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.115 NA.9: 1 residues within 4Å: Chain D: P.240 No protein-ligand interaction detected (PLIP) NA.10: 1 residues within 4Å: Chain F: C.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pence, M.G. et al., Lesion bypass of N2-ethylguanine by human DNA polymerase iota. J.Biol.Chem. (2009)

Release Date

2008-12-16

Peptides

DNA polymerase iota: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

DNA polymerase iota

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