SMTL ID : 4ru9.1

Crystal structure of human DNA polymerase eta inserting dCMPNPP opposite a MeFapy-dG adducted DNA template

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DG- DT- DC- DA- DT: Nucleic acids Primar: AGCGTCAT(Non-covalent)

DA-DG-DC-DG-DT-DC-DA-DT.1: 27 residues within 4Å: Chain A: S.113, D.115, E.116, K.224, R.256, S.257, L.258, G.259, G.260, K.261, L.262, L.378, S.380, L.381, R.382, R.383, C.384 Chain B: A.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: 17 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, D.115, K.231 Chain B: X.4 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.18 Hydrogen bonds: A:C.16, A:F.17, A:F.18, A:Y.52, A:R.61, A:R.61 Water bridges: A:D.13, A:R.55, A:R.55, A:R.55, A:R.55 Salt bridges: A:R.55, A:K.231

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.13, M.14, D.115 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: 6 residues within 4Å: Chain A: D.13, D.115, E.116 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.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.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patra, A. et al., Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase eta and Sulfolobus solfataricus P2 Polymerase IV. J.Am.Chem.Soc. (2015)

Release Date

2015-08-05

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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