SMTL ID : 3mr2.1

Human DNA polymerase eta in complex with normal DNA and incoming nucleotide (Nrm)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

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

DT-DA-DG-DC-DG-DT-DC-DA-DT.1: 30 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, Q.368, R.380, L.384, R.385, R.386, C.387, K.431 Chain B: A.6, T.7, G.8, A.9, C.10, G.11, C.12, T.13 Ligands: DZ4.2, MG.4, GOL.7 Protein-ligand interaction information (PLIP) not available

2 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.2: 19 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: T.5, A.6 Ligands: DT-DA-DG-DC-DG-DT-DC-DA-DT.1, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:M.17, A:C.19, A:F.20, A:F.21, A:Y.55, A:R.58, A:R.64 Water bridges: A:D.16, A:R.58, A:R.58, A:S.116 Salt bridges: A:R.58, A:K.234 DZ4.10: 5 residues within 4Å: Chain A: S.260, L.265, K.296, N.297, W.300 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.260, A:K.296, A:N.297 pi-Stacking: A:W.300, A:W.300, A:W.300 pi-Cation interactions: A:K.296

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: DZ4.2, 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-DA-DG-DC-DG-DT-DC-DA-DT.1, DZ4.2, 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.1

6 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: Q.23, Q.26, R.27, R.33, G.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.23 Water bridges: A:Q.26 GOL.7: 7 residues within 4Å: Chain A: D.16, E.119, K.227, C.230, G.231, K.234 Ligands: DT-DA-DG-DC-DG-DT-DC-DA-DT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.119, A:K.227, A:K.227 GOL.8: 3 residues within 4Å: Chain A: N.29, P.30, H.31 No protein-ligand interaction detected (PLIP) GOL.9: 6 residues within 4Å: Chain A: Q.41, Y.42, K.43, Q.82, V.83, E.85 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.42, A:K.43, A:Q.82, A:V.83, A:V.83, A:E.85 GOL.11: 5 residues within 4Å: Chain A: T.321, F.426 Chain B: G.8, A.9, C.10 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.321, A:T.321, A:T.321, A:R.385

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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