SMTL ID : 6vf1.1

DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mg2+ (120 min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

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

DC-DG-DG-DC-DA-DT-DA-DC-DG.1: 24 residues within 4Å: Chain A: G.48, L.51, H.239, F.259, E.260, R.261, K.300, R.304, R.307, R.308, R.311, K.312, L.318, N.319, H.321 Ligands: DC-DG-DT-DA-8GM.2, DC-DG-DT-DA-8GM.2, DC-DG-DT-DA-8GM.2, DC-DG-DT-DA-8GM.2, DC-DG-DT-DA-8GM.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3 Protein-ligand interaction information (PLIP) not available

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

DC-DG-DT-DA-8GM.2: 31 residues within 4Å: Chain A: I.117, F.118, G.119, V.120, G.121, K.123, T.124, Q.149, R.197, D.204, D.206, F.263, R.278, D.280, G.295, W.296, T.297, G.298, S.299, K.300, Q.303 Ligands: DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DG-DC-DA-DT-DA-DC-DG.1, MG.4, MG.5, NA.6, GOA.9, EDO.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.197, A:D.280, A:S.299, A:K.300 Water bridges: A:R.197, A:D.204

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.48, R.49, T.52, F.53, P.77, H.78, G.80, E.81, H.82, S.83 Ligands: DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DG-DC-DA-DT-DA-DC-DG.1 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.204, D.206 Ligands: DC-DG-DT-DA-8GM.2, MG.5, GOA.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.1, H2O.1 MG.5: 6 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: DC-DG-DT-DA-8GM.2, DC-DG-DT-DA-8GM.2, MG.4 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

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

NA.6: 4 residues within 4Å: Chain A: T.115, I.117, V.120 Ligands: DC-DG-DT-DA-8GM.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.115, A:V.120 NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.7: 4 residues within 4Å: Chain A: S.46, E.47, G.48, R.49 Ligand excluded by PLIP

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

DTT.8: 3 residues within 4Å: Chain A: E.35, A.38, C.54 No protein-ligand interaction detected (PLIP)

1 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.9: 7 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, D.206 Ligands: DC-DG-DT-DA-8GM.2, MG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.194, A:D.204 Water bridges: A:R.197 Salt bridges: A:R.197

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

EPE.10: 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 7 residues within 4Å: Chain A: R.261, G.295, W.296, R.307, S.320 Ligands: DC-DG-DT-DA-8GM.2, DC-DG-DT-DA-8GM.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.261, A:R.261, A:G.295, A:R.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamsen, J.A. et al., DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mg2+ (120 min). To be published

Release Date

2021-09-01

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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