SMTL ID : 7ktk.1

DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Ground State Ternary Complex, 50 mM Mg2+ (90min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 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, H.239, F.259, E.260, R.261, R.304, R.307, R.308, R.311, K.312, L.318, N.319, H.321 Ligands: DC-DG-DT-DA.2, DC-DG-DT-DA.2, DC-DG-DT-DA.2, DC-DG-DT-DA.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, 8DG.4, EDO.16, EDO.18, EDO.19 Protein-ligand interaction information (PLIP) not available

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

DC-DG-DT-DA.2: 19 residues within 4Å: Chain A: I.117, F.118, G.119, V.120, G.121, K.123, T.124, Q.149, H.203, F.263, R.278 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, 8DG.4, NA.7, EDO.18 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: 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, EDO.19 Protein-ligand interaction information (PLIP) not available

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

8DG.4: 20 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, D.300, R.307 Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DT-DA.2, MG.5, MG.6, EDO.14, EDO.18 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.194, A:R.197, A:H.203, A:D.204, A:D.204, A:R.307, A:R.307 Water bridges: A:R.197, A:R.197, A:R.197, A:R.197, A:K.199, A:K.199, A:D.300 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203, A:H.203, A:D.300

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: 8DG.4, MG.6 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.12 MG.6: 4 residues within 4Å: Chain A: D.204, D.206 Ligands: 8DG.4, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.5

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

NA.7: 4 residues within 4Å: Chain A: T.115, I.117, V.120 Ligands: DC-DG-DT-DA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.115, A:V.120

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

EPE.8: 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

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

EDO.9: 5 residues within 4Å: Chain A: L.63, P.64, S.65, P.66, Q.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.65 Water bridges: A:Q.72 EDO.10: 7 residues within 4Å: Chain A: F.43, E.44, G.45, R.107, V.122, K.123, D.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.43, A:R.107 EDO.11: 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:T.210 EDO.12: 6 residues within 4Å: Chain A: S.287, F.291, H.321, G.322, F.331, Q.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.321, A:Q.333, A:Q.333 EDO.13: 8 residues within 4Å: Chain A: E.217, A.218, G.219, L.220, L.221, P.222, F.259, V.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.219, A:L.220, A:L.221 EDO.14: 5 residues within 4Å: Chain A: C.54, D.300, L.301, R.304 Ligands: 8DG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.304 EDO.15: 4 residues within 4Å: Chain A: E.35, C.54, K.61, A.356 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.356 EDO.16: 4 residues within 4Å: Chain A: N.319, H.321 Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.319, A:N.319 EDO.17: 3 residues within 4Å: Chain A: K.312, E.313, G.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.312 EDO.18: 7 residues within 4Å: Chain A: G.295, W.296, R.307, S.320 Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DT-DA.2, 8DG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.295, A:R.307, A:R.307 EDO.19: 4 residues within 4Å: Ligands: DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DC-DG-DG-DC-DC-DT-DA-DC-DG.1, DG-DC-DC-DG.3, DG-DC-DC-DG.3 No protein-ligand interaction detected (PLIP)

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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