SMTL ID : 5vze.1

Post-catalytic complex of human Polymerase Mu (W434A) mutant with incoming UTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 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.46, L.49, Q.236, H.237, F.257, E.258, R.259, F.261, R.302, R.305, R.306, R.309, K.310, L.316, N.317, H.319 Ligands: DC-DG-DT-DA-U.2, DC-DG-DT-DA-U.2, DC-DG-DT-DA-U.2, DC-DG-DT-DA-U.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, UTP.8 Protein-ligand interaction information (PLIP) not available

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

DC-DG-DT-DA-U.2: 20 residues within 4Å: Chain A: T.113, I.115, F.116, G.117, V.118, G.119, K.121, T.122, Q.147, H.201, F.261, R.276 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, NA.6, UTP.8, GOA.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.3: 16 residues within 4Å: Chain A: A.12, G.46, R.47, T.50, F.51, P.75, H.76, F.77, G.78, E.79, H.80, S.81 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)(Non-functional Binders)

MG.4: 6 residues within 4Å: Chain A: D.202, D.204, D.278 Ligands: MG.5, UTP.8, GOA.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.202, A:D.204, A:D.278 MG.5: 4 residues within 4Å: Chain A: D.202, D.204 Ligands: MG.4, UTP.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:D.204, H2O.5 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.6: 5 residues within 4Å: Chain A: T.113, I.115, V.118 Ligands: DC-DG-DT-DA-U.2, DC-DG-DT-DA-U.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.113, A:V.118

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

CL.7: 3 residues within 4Å: Chain A: Q.16, L.344, E.345 Ligand excluded by PLIP

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.8: 19 residues within 4Å: Chain A: G.191, G.192, R.195, K.197, G.200, H.201, D.202, D.204, G.293, A.294, T.295, G.296, K.298, Q.301 Ligands: DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DT-DA-U.2, MG.4, MG.5, GOA.9 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.192, A:R.195, A:H.201, A:D.202, A:D.204, A:G.293 Water bridges: A:R.195, A:R.195, A:R.195, A:K.197, A:K.197, A:K.197, A:K.197, A:H.201, A:D.202, A:D.202, A:R.305 Salt bridges: A:R.195, A:K.197, A:K.197, A:H.201, A:H.201

1 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.9: 9 residues within 4Å: Chain A: H.201, D.202, D.204, R.276, D.278 Ligands: DC-DG-DT-DA-U.2, DC-DG-DT-DA-U.2, MG.4, UTP.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.202, A:R.276, A:D.278

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

EDO.10: 5 residues within 4Å: Chain A: L.61, P.62, S.63, P.64, Q.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, A.F. et al., Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu. Nucleic Acids Res. (2017)

Release Date

2017-07-05

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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