SMTL ID : 7ktm.1

DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Reaction State Ternary Complex, 50 mM Mn2+ (30min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

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

DC-DG-DG-DC-DC-DT-DA-DC-DG.1: 27 residues within 4Å: Chain A: G.48, L.51, Q.238, F.259, E.260, R.261, F.263, R.304, R.307, R.308, R.311, K.312, L.318, N.319, H.321 Ligands: DC-DG-DT-DA-8OG.2, DC-DG-DT-DA-8OG.2, DC-DG-DT-DA-8OG.2, DC-DG-DT-DA-8OG.2, DC-DG-DT-DA-8OG.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, 8DG.10, EDO.13, MN.17 Protein-ligand interaction information (PLIP) not available

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

DC-DG-DT-DA-8OG.2: 35 residues within 4Å: Chain A: I.117, F.118, G.119, V.120, G.121, K.123, T.124, Q.149, G.193, R.197, H.203, D.204, D.206, F.263, R.278, D.280, G.295, W.296, T.297, G.298, S.299, D.300, R.307 Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, MN.4, MN.9, 8DG.10, PPV.11, EDO.12, MN.18, MN.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.197, A:R.307 Water bridges: A:D.300, A:D.300 Salt bridges: A:H.203

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

DG-DC-DC-DG.3: 16 residues within 4Å: Chain A: G.48, R.49, T.52, F.53, P.77, H.78, G.80, E.81, H.82, S.83 Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, MN.8, MN.20 Protein-ligand interaction information (PLIP) not available

10 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.4: 6 residues within 4Å: Chain A: D.204, D.206 Ligands: DC-DG-DT-DA-8OG.2, 8DG.10, PPV.11, MN.19 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.5 MN.5: 2 residues within 4Å: Chain A: E.260, H.321 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.260, A:H.321, H2O.7, H2O.9, H2O.12 MN.6: 1 residues within 4Å: Chain A: H.93 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.93, H2O.9, H2O.10 MN.7: 1 residues within 4Å: Chain A: H.26 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.26, H2O.3, H2O.9, H2O.11 MN.8: 2 residues within 4Å: Chain A: H.82 Ligands: DG-DC-DC-DG.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.82, H2O.2, H2O.15 MN.9: 4 residues within 4Å: Chain A: T.115, I.117, V.120 Ligands: DC-DG-DT-DA-8OG.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.115, A:I.117, A:V.120, H2O.13, H2O.14 MN.17: 1 residues within 4Å: Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1 No protein-ligand interaction detected (PLIP) MN.18: 3 residues within 4Å: Ligands: DC-DG-DT-DA-8OG.2, 8DG.10, PPV.11 No protein-ligand interaction detected (PLIP) MN.19: 6 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: DC-DG-DT-DA-8OG.2, MN.4, 8DG.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.5, H2O.5 MN.20: 1 residues within 4Å: Ligands: DG-DC-DC-DG.3 No protein-ligand interaction detected (PLIP)

1 x 8DG: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8DG.10: 24 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, G.202, H.203, D.204, D.206, G.295, W.296, T.297, G.298, S.299, D.300, R.307 Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DT-DA-8OG.2, DC-DG-DT-DA-8OG.2, MN.4, PPV.11, EDO.12, MN.18, MN.19 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.194, A:R.197, A:H.203, A:D.204, A:R.307 Water bridges: A:R.197, A:R.197, A:R.197, A:R.197, A:H.203, A:H.203, A:D.204, A:D.204 Salt bridges: A:R.197, A:K.199, A:H.203, A:H.203

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.11: 12 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, G.202, H.203, D.204, D.206 Ligands: DC-DG-DT-DA-8OG.2, MN.4, 8DG.10, MN.18 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.194, A:H.203 Water bridges: A:F.195, A:R.197, A:R.197, A:R.197, A:R.197, A:D.204, A:D.204 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203

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

EDO.12: 8 residues within 4Å: Chain A: R.261, G.295, W.296, R.307, S.320 Ligands: DC-DG-DT-DA-8OG.2, 8DG.10, EDO.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.261, A:R.261, A:G.295, A:R.307 EDO.13: 8 residues within 4Å: Chain A: R.261, R.307, N.319, S.320, H.321 Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.261, A:S.320 EDO.14: 3 residues within 4Å: Chain A: T.188, T.210, F.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.188 Water bridges: A:V.286 EDO.15: 2 residues within 4Å: Chain A: H.321, F.331 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.331

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

EPE.16: 4 residues within 4Å: Chain A: L.23, K.199, L.200, Q.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.200, A:Q.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamsen, J.A. et al., Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide. Nat Commun (2021)

Release Date

2022-05-11

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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