SMTL ID : 4j9k.1

Human DNA polymerase eta-DNA ternary complex: misincorporation G opposite T after a T at the primer 3' end (TA/G)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DG- DT- DC- DA- DT: DNA(Non-covalent)

DA-DG-DC-DG-DT-DC-DA-DT.1: 28 residues within 4Å: Chain A: R.64, 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: T.5, A.6, T.7, G.8, A.9, C.10, G.11, C.12, T.13 Ligands: XG4.4, GOL.9, GOL.10, GOL.11 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: MG.3, XG4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.3: 6 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: MG.2, XG4.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.6, H2O.9

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: T.5, A.6 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:M.17, A:C.19, A:F.20, A:F.21, A:Q.41, A:Q.41, A:Y.55, A:R.64 Water bridges: A:Y.55, A:R.58, A:R.58, A:R.58, A:S.116 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:K.296 Water bridges: A:E.309, A:D.311 pi-Stacking: A:W.300, A:W.300 pi-Cation interactions: A:K.296, A:W.300

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280, T.282 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.280 GOL.6: 5 residues within 4Å: Chain A: Y.149, E.151, G.152, L.153, M.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.152 GOL.8: 6 residues within 4Å: Chain A: T.321, F.426, C.428 Chain B: G.8, A.9, C.10 No protein-ligand interaction detected (PLIP) GOL.9: 6 residues within 4Å: Chain A: V.370, R.385, C.387 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, DA-DG-DC-DG-DT-DC-DA-DT.1, DA-DG-DC-DG-DT-DC-DA-DT.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.385 GOL.10: 5 residues within 4Å: Chain B: G.8, A.9, C.10 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, DA-DG-DC-DG-DT-DC-DA-DT.1 No protein-ligand interaction detected (PLIP) GOL.11: 4 residues within 4Å: Chain B: T.13 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, DA-DG-DC-DG-DT-DC-DA-DT.1, DA-DG-DC-DG-DT-DC-DA-DT.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-05-01

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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