SMTL ID : 7ktc.1

DNA Polymerase Mu, 8-oxodGTP:Ct Product State Ternary Complex, 10 mM Mn2+ (120min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: 26 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, EDO.13, MN.19 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: 34 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, K.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, NA.4, MN.5, MN.6, PPV.11, EDO.12, MN.20 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.197, A:R.307 Water bridges: A:H.203, A:D.204, A:K.300, A:K.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: 15 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.21 Protein-ligand interaction information (PLIP) not available

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

NA.4: 4 residues within 4Å: Chain A: T.115, I.117, V.120 Ligands: DC-DG-DT-DA-8OG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.115, A:V.120

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

MN.5: 6 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: DC-DG-DT-DA-8OG.2, DC-DG-DT-DA-8OG.2, MN.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.1 MN.6: 5 residues within 4Å: Chain A: D.204, D.206 Ligands: DC-DG-DT-DA-8OG.2, MN.5, PPV.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.5 MN.7: 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.8, H2O.11 MN.8: 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.9, H2O.10, H2O.13 MN.19: 1 residues within 4Å: Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1 No protein-ligand interaction detected (PLIP) MN.20: 2 residues within 4Å: Ligands: DC-DG-DT-DA-8OG.2, PPV.11 No protein-ligand interaction detected (PLIP) MN.21: 1 residues within 4Å: Ligands: DG-DC-DC-DG.3 No protein-ligand interaction detected (PLIP)

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

EPE.9: 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

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.10: 1 residues within 4Å: Chain A: C.54 No protein-ligand interaction detected (PLIP)

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.11: 11 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.6, MN.20 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.194, A:H.203 Water bridges: A:R.197, A:R.197, A:R.197, A:K.199, A:K.199 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203

7 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, DC-DG-DT-DA-8OG.2, EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.261, A:R.261, 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.319 Hydrogen bonds: A:R.261, A:R.307, A:R.307 EDO.14: 3 residues within 4Å: Chain A: T.188, T.210, F.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.188 Water bridges: A:T.210, A:V.286 EDO.15: 3 residues within 4Å: Chain A: Q.288, H.321, F.331 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.288 EDO.16: 8 residues within 4Å: Chain A: E.217, A.218, G.219, L.220, L.221, P.222, F.259, V.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.219, A:L.220, A:L.221 Water bridges: A:F.259 EDO.17: 6 residues within 4Å: Chain A: S.167, D.168, A.171, L.268, P.269, Q.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.168, A:D.168 Water bridges: A:A.171, A:Q.270 EDO.18: 2 residues within 4Å: Chain A: R.127, R.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.130, A:R.130

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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