SMTL ID : 4rnn.1

Crystal structure of human polymerase eta inserting dGMPnPP opposite DNA template containing an abasic site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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: 29 residues within 4Å: Chain A: R.64, 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.381, L.384, R.385, R.386, C.387 Chain B: A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: XG4.2, MG.4 Protein-ligand interaction information (PLIP) not available

1 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.2: 20 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, Q.41, I.51, A.52, Y.55, R.58, R.64, I.117, D.118, K.234 Chain B: N.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:D.16, A:D.18, A:C.19, A:F.20, A:F.21, A:Q.41, A:Q.41, A:Y.55, A:R.64 Water bridges: A:D.16, A:R.58, A:R.58, A:R.58, A:R.58, A:R.58, A:S.116 Salt bridges: A:R.58, A:K.234

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: XG4.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.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, XG4.2, MG.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.7

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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 GOL.6: 5 residues within 4Å: Chain A: G.274, I.275, E.276, Y.277, E.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.274, A:E.276 Water bridges: A:E.276, A:E.280 GOL.7: 5 residues within 4Å: Chain A: Q.23, Q.26, R.27, R.33, G.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.23, A:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patra, A. et al., Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase eta. J.Biol.Chem. (2015)

Release Date

2015-02-18

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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