SMTL ID : 3mr6.1

Human DNA polymerase eta - DNA ternary complex with a CPD 2bp upstream of the active site (TT4)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

DT-DC-DT-DC-DG-DT-DA-DA-DT.1: 30 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, Q.368, R.380, L.381, L.384, R.385, R.386, C.387, K.431 Chain B: C.4, A.5, T.6, A.7, C.8, G.9, A.10, G.11 Ligands: XG4.2, MG.4 Protein-ligand interaction information (PLIP) not available

2 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, I.51, A.52, Y.55, R.58, R.64, I.117, D.118, K.234 Chain B: C.4, A.5 Ligands: DT-DC-DT-DC-DG-DT-DA-DA-DT.1, MG.3, MG.4, GOL.7 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:M.17, A:D.18, A:C.19, A:F.20, A:F.21, A:R.64 Water bridges: A:D.16, A:Q.41, A:Q.41, A:R.58, A:R.58, A:R.58, A:R.58, A:R.64, A:S.116, A:K.227 Salt bridges: A:R.58, A:K.234 XG4.12: 4 residues within 4Å: Chain A: S.260, K.296, N.297, W.300 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.260, A:S.260 Water bridges: A:E.309, A:D.311 pi-Stacking: A:W.300, A:W.300, A:W.300 pi-Cation interactions: A:W.300

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: DT-DC-DT-DC-DG-DT-DA-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.2

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.96, V.100, L.318, P.319, N.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.362, A:N.362 Water bridges: A:R.114 GOL.6: 5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain A: Y.55, R.58, G.231, K.234 Ligands: XG4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.55, A:Y.55, A:R.58 GOL.8: 4 residues within 4Å: Chain A: N.29, L.32, L.80, A.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:L.80 Water bridges: A:Q.82 GOL.9: 7 residues within 4Å: Chain A: S.107, A.110, V.111, I.112, P.315, R.316, Q.317 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.112 GOL.10: 3 residues within 4Å: Chain A: Q.283, F.284, Q.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.283, A:Q.288, A:Q.288 GOL.11: 3 residues within 4Å: Chain A: E.97, A.98, E.101 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.94, A:E.97, A:E.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biertumpfel, C. et al., Structure and mechanism of human DNA polymerase eta. Nature (2010)

Release Date

2010-06-30

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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