SMTL ID : 6p1o.1

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated dAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x DC- DG- DG- DC- 8OG- DT- DA- DC- DG: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3')(Non-covalent)

DC-DG-DG-DC-8OG-DT-DA-DC-DG.1: 25 residues within 4Å: Chain A: G.46, L.49, R.53, F.257, E.258, R.259, F.261, R.302, R.305, R.306, R.309, K.310, L.316, N.317, H.319 Ligands: DC-DG-DT-DA-DA.2, DC-DG-DT-DA-DA.2, DC-DG-DT-DA-DA.2, DC-DG-DT-DA-DA.2, DC-DG-DT-DA-DA.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, CL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.302, A:R.305 Salt bridges: A:R.302 pi-Cation interactions: A:R.302

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

DC-DG-DT-DA-DA.2: 31 residues within 4Å: Chain A: I.115, F.116, G.117, V.118, G.119, K.121, T.122, Q.147, R.195, H.201, D.202, D.204, F.261, R.276, D.278, G.293, W.294, T.295, G.296, K.298 Ligands: DC-DG-DG-DC-8OG-DT-DA-DC-DG.1, DC-DG-DG-DC-8OG-DT-DA-DC-DG.1, DC-DG-DG-DC-8OG-DT-DA-DC-DG.1, DC-DG-DG-DC-8OG-DT-DA-DC-DG.1, DC-DG-DG-DC-8OG-DT-DA-DC-DG.1, MN.4, MG.5, NA.6, PPV.10, EDO.11, ATP.13 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: DNA (5'-D(P*GP*CP*CP*G)-3')(Non-covalent)

DG-DC-DC-DG.3: 14 residues within 4Å: Chain A: G.46, R.47, T.50, F.51, P.75, H.76, G.78, E.79, H.80, S.81 Ligands: DC-DG-DG-DC-8OG-DT-DA-DC-DG.1, DC-DG-DG-DC-8OG-DT-DA-DC-DG.1, DC-DG-DG-DC-8OG-DT-DA-DC-DG.1, DC-DG-DG-DC-8OG-DT-DA-DC-DG.1 Protein-ligand interaction information (PLIP) not available

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 6 residues within 4Å: Chain A: D.202, D.204, D.278 Ligands: DC-DG-DT-DA-DA.2, DC-DG-DT-DA-DA.2, MG.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.202, A:D.204, A:D.278

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: D.202, D.204 Ligands: DC-DG-DT-DA-DA.2, MN.4, PPV.10, ATP.13 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:D.204, H2O.6

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: T.113, I.115, V.118 Ligands: DC-DG-DT-DA-DA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.113, A:V.118

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: R.259, R.305, N.317, S.318 Ligands: DC-DG-DG-DC-8OG-DT-DA-DC-DG.1 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: S.44, E.45, G.46, R.47 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.265, W.272 Ligand excluded by PLIP

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.10: 9 residues within 4Å: Chain A: G.191, G.192, R.195, H.201, D.202, D.204 Ligands: DC-DG-DT-DA-DA.2, MG.5, ATP.13 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.192 Water bridges: A:R.195, A:R.195, A:R.195, A:K.197, A:K.197, A:H.201, A:D.202, A:D.202 Salt bridges: A:R.195, A:H.201

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 7 residues within 4Å: Chain A: R.259, G.293, W.294, R.305, S.318 Ligands: DC-DG-DT-DA-DA.2, DC-DG-DT-DA-DA.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.259, A:R.259, A:R.305, A:R.305

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 4 residues within 4Å: Chain A: L.21, K.197, L.198, Q.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.198, A:Q.199 Salt bridges: A:K.197

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.13: 9 residues within 4Å: Chain A: G.191, G.192, R.195, H.201, D.202, D.204 Ligands: DC-DG-DT-DA-DA.2, MG.5, PPV.10 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.192, A:K.197, A:D.202 Water bridges: A:R.195, A:R.195, A:R.195, A:R.195, A:H.201, A:H.201 Salt bridges: A:R.195, A:K.197, A:H.201, A:H.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaminski, A.M. et al., Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine. Nucleic Acids Res. (2019)

Release Date

2019-09-04

Peptides

DNA-directed DNA/RNA polymerase mu: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA/RNA polymerase mu

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