SMTL ID : 4m0a.1

Human DNA Polymerase Mu post-catalytic complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x DC- DG- DG- DC- DA- DT- DA- DC- DG: template strand(Non-covalent)

DC-DG-DG-DC-DA-DT-DA-DC-DG.1: 24 residues within 4Å: Chain A: G.48, L.51, 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: upstream primer strand(Non-covalent)

DC-DG-DT-DA-DT.2: 29 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, PPV.6, MN.8, EDO.12 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: downstream primer strand(Non-covalent)

DG-DC-DC-DG.3: 16 residues within 4Å: Chain A: A.14, G.48, R.49, T.52, F.53, R.55, 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

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.204, D.206 Ligands: DC-DG-DT-DA-DT.2, PPV.6, MN.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.1, H2O.12 MG.5: 4 residues within 4Å: Chain A: T.115, I.117, V.120 Ligands: DC-DG-DT-DA-DT.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.6, H2O.14 MG.9: 2 residues within 4Å: Chain A: D.204 Ligands: PPV.6 No protein-ligand interaction detected (PLIP)

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.6: 8 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, D.206 Ligands: DC-DG-DT-DA-DT.2, MG.4, MG.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.194 Water bridges: A:F.195, A:R.197, A:R.197, A:R.197, A:D.206 Salt bridges: A:R.197, A:R.197, A:K.199

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

EDO.7: 5 residues within 4Å: Chain A: L.63, P.64, S.65, P.66, Q.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.65 EDO.10: 3 residues within 4Å: Chain A: T.188, T.210, F.289 No protein-ligand interaction detected (PLIP) EDO.12: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.261, A:R.261, A:R.307, A:R.307

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 6 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 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.15

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

EPE.11: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, A.F. et al., Sustained active site rigidity during synthesis by human DNA polymerase mu. Nat.Struct.Mol.Biol. (2014)

Release Date

2014-02-05

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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