SMTL ID : 4yd2.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

1 x DC- DG- DT- DA- DT: DNA (5'-D(*CP*GP*TP*AP*T)-3')(Non-covalent)

DC-DG-DT-DA-DT.1: 27 residues within 4Å: Chain A: I.115, F.116, G.117, V.118, G.119, K.121, T.122, Q.147, R.195, D.202, D.204, R.259, F.261, R.276, D.278, G.293, W.294, T.295, G.296, S.297, K.298 Chain B: A.5, A.6 Ligands: NA.3, NA.6, NA.7, PPV.9 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: 16 residues within 4Å: Chain A: G.46, R.47, T.50, F.51, R.53, P.75, H.76, F.77, 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

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

NA.3: 6 residues within 4Å: Chain A: D.202, D.204, D.278 Ligands: DC-DG-DT-DA-DT.1, DC-DG-DT-DA-DT.1, NA.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.278 NA.6: 5 residues within 4Å: Chain A: D.202, D.204 Ligands: DC-DG-DT-DA-DT.1, NA.3, PPV.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.202 Water bridges: A:G.192 NA.7: 6 residues within 4Å: Chain A: T.113, Q.114, I.115, F.116, V.118 Ligands: DC-DG-DT-DA-DT.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.114

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

CL.4: 4 residues within 4Å: Chain A: L.21, K.197, L.198, Q.199 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: L.291, S.334, E.335 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: S.44, E.45, G.46, R.47 Ligand excluded by PLIP

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.9: 6 residues within 4Å: Chain A: G.191, G.192, R.195, D.204 Ligands: DC-DG-DT-DA-DT.1, NA.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.192 Water bridges: A:R.195, A:R.195, A:K.197, A:D.204 Salt bridges: A:R.195, A:K.197

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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