SMTL ID : 4q8f.1

Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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

DA-DG-DT-DG-DT-DG-DA-DC.1: 25 residues within 4Å: Chain A: R.64, S.116, D.118, E.119, K.227, R.259, S.260, L.261, G.262, G.263, K.264, L.265, R.385, R.386, C.387 Chain B: X.4, T.5, C.6, A.7, C.8, A.9, C.10, T.11 Ligands: MG.3, XG4.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.67 Hydrogen bonds: A:G.49, A:K.320, A:T.321, A:G.323, A:S.325 Water bridges: A:I.50, A:S.65, A:K.89, A:R.96, A:N.297 Salt bridges: A:K.89, A:R.96, A:K.296, A:K.314, A:R.316, A:K.320, A:R.354

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: MG.3, XG4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.16, A:D.16, A:M.17, A:D.118 MG.3: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DT-DG-DT-DG-DA-DC.1, MG.2, XG4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.1

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

XG4.4: 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: C.3, X.4 Ligands: DA-DG-DT-DG-DT-DG-DA-DC.1, MG.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:C.19, A:F.20, A:F.21, A:Y.55, A:R.64 Water bridges: A:Q.41, A:K.227, A:K.227 Salt bridges: A:R.58, A:K.234 XG4.7: 4 residues within 4Å: Chain A: S.260, K.296, N.297, W.300 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.260, A:S.260, A:S.260 Water bridges: A:W.300 pi-Stacking: A:W.300, A:W.300, A:W.300 pi-Cation interactions: A:W.300, A:W.300

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 No protein-ligand interaction detected (PLIP) GOL.6: 5 residues within 4Å: Chain A: R.27, K.94, E.97, A.98, E.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.27, A:K.94, A:E.97, A:E.101 GOL.8: 6 residues within 4Å: Chain A: S.325, N.327, R.374, M.424 Chain B: X.4, T.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.325, A:S.325, A:N.327, A:R.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gregory, M.T. et al., Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-07-02

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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