SMTL ID : 5tye.1

DNA Polymerase Mu Product Complex, 10 mM Mg2+ (60 min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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: 25 residues within 4Å: Chain A: G.48, L.51, Q.238, F.259, E.260, R.261, F.263, K.300, R.304, R.307, R.308, R.311, K.312, L.318, N.319, H.321 Ligands: DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.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- DT: DNA (5'-D(*CP*GP*TP*AP*T)-3')(Non-covalent)

DC-DG-DT-DA-DT.2: 30 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, K.300 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, NA.7, EDO.8, PPV.15 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: 16 residues within 4Å: Chain A: A.14, 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, EDO.10 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.204, D.206 Ligands: DC-DG-DT-DA-DT.2, MG.5, NA.6, PPV.15 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.3, H2O.5 MG.5: 7 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, MG.4, NA.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.2

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

NA.6: 7 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, MG.4, MG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.204 Water bridges: A:R.278 NA.7: 4 residues within 4Å: Chain A: T.115, I.117, V.120 Ligands: DC-DG-DT-DA-DT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.115, A:G.119, A:V.120

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

EDO.8: 6 residues within 4Å: Chain A: R.261, G.295, W.296, R.307 Ligands: DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.307, A:R.307 Water bridges: A:S.320 EDO.9: 3 residues within 4Å: Chain A: Q.288, H.321, F.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.288 Water bridges: A:N.319, A:H.321 EDO.10: 4 residues within 4Å: Chain A: Y.15, Q.18, E.313 Ligands: DG-DC-DC-DG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.18 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, A:T.188 EDO.12: 2 residues within 4Å: Chain A: T.28, G.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.28, A:G.29

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

DTT.13: 1 residues within 4Å: Chain A: C.54 No protein-ligand interaction detected (PLIP)

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

EPE.14: 4 residues within 4Å: Chain A: L.23, K.199, L.200, Q.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.200, A:Q.201 Salt bridges: A:K.199

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.15: 8 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, D.204, D.206 Ligands: DC-DG-DT-DA-DT.2, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.194 Water bridges: A:R.197, A:R.197, A:R.197, A:R.197, A:K.199, A:K.199, A:D.204 Salt bridges: A:R.197, A:K.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamsen, J.A. et al., Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Nat Commun (2017)

Release Date

2017-08-30

Peptides

DNA-directed DNA/RNA polymerase mu: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA/RNA polymerase mu

Related Entries With Identical Sequence