SMTL ID : 4o3s.1

Crystal structure of human polymerase eta extending an 8-oxog dna lesion: post insertion of 8-oxog-dc pair

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-DC.1: 28 residues within 4Å: Chain A: S.113, D.115, E.116, K.224, I.255, R.256, S.257, L.258, G.259, G.260, K.261, L.262, R.377, L.381, R.382, R.383, C.384 Chain B: G.4, G.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: 0KX.2, MG.4 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: D.13, M.14, D.15, C.16, F.17, F.18, I.48, A.49, Y.52, R.55, R.61, I.114, D.115, K.231 Chain B: G.4, G.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DC.1, MG.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.18 Hydrogen bonds: A:D.13, A:C.16, A:F.17, A:F.18, A:R.55, A:R.61, A:R.61 Water bridges: A:D.13, A:Y.52, A:R.55, A:R.55, A:R.55, A:K.224 Salt bridges: A:R.55, A:K.231

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.13, M.14, D.115, K.231 Ligands: 0KX.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.13, A:M.14, A:D.115 MG.4: 7 residues within 4Å: Chain A: D.13, S.113, D.115, E.116 Ligands: DA-DG-DC-DG-DT-DC-DA-DC.1, 0KX.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.13, A:D.115, A:E.116, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: P.244, F.247, S.248, G.276, E.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patra, A. et al., Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta. J.Biol.Chem. (2014)

Release Date

2014-04-30

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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