SMTL ID : 4yr0.1

Mutant Human DNA Polymerase Eta R61M Inserting dCTP Opposite an 8-Oxoguanine Lesion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DG- DT- DC- DA- DT: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')(Non-covalent)

DA-DG-DC-DG-DT-DC-DA-DT.1: 28 residues within 4Å: Chain A: S.116, D.118, E.119, K.227, I.258, R.259, S.260, L.261, G.262, G.263, K.264, L.265, R.380, L.384, R.385, R.386, C.387 Chain B: G.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: DCP.2, CA.4 Protein-ligand interaction information (PLIP) not available

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

DCP.2: 18 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, I.51, A.52, Y.55, R.58, M.64, I.117, D.118, K.234 Chain B: G.4 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, CA.3, CA.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:C.19, A:F.20, A:F.21, A:Y.55, A:D.118, A:D.118 Water bridges: A:D.18, A:R.58, A:R.58, A:R.58, A:S.116, A:D.118, A:K.234, A:K.234 Salt bridges: A:R.58, A:R.58, A:K.234

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: DCP.2, CA.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.16, A:D.16, A:M.17, A:D.118 CA.4: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, DCP.2, CA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.10

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: E.97, A.98, E.101 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.97, A:A.98, A:E.101 GOL.6: 5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, Y. et al., Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine. J.Biol.Chem. (2015)

Release Date

2015-05-13

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

Related Entries With Identical Sequence