SMTL ID : 4ycx.1

Binary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

DC-DG-DT-DA.1: 20 residues within 4Å: Chain A: F.116, G.117, V.118, G.119, K.121, T.122, Q.147, Q.238, R.259, F.261, R.276, D.278, W.294 Chain B: A.6, T.7, A.8, C.9, G.10 Ligands: NA.4, IMD.7 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.2: 14 residues within 4Å: Chain A: G.46, R.47, T.50, F.51, P.75, H.76, G.78, E.79, H.80, S.81 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.202, D.204, D.278 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.204, A:D.278, H2O.2, H2O.2, H2O.11

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

NA.4: 2 residues within 4Å: Chain A: T.113 Ligands: DC-DG-DT-DA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.113

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: T.186, T.208, F.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.186 Water bridges: A:T.208 GOL.6: 4 residues within 4Å: Chain A: W.315, F.322, F.329 Chain B: T.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.317 GOL.8: 2 residues within 4Å: Chain B: A.6, T.7 No protein-ligand interaction detected (PLIP)

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 4 residues within 4Å: Chain A: G.293, W.294, S.318 Ligands: DC-DG-DT-DA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.318 Water bridges: A:R.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, A.F. et al., Creative template-dependent synthesis by human polymerase mu. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-08-05

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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