SMTL ID : 5vza.1

Pre-catalytic ternary complex of human Polymerase Mu (G433S) mutant with incoming nonhydrolyzable UMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: 26 residues within 4Å: Chain A: G.46, L.49, Q.236, H.237, F.257, E.258, R.259, F.261, K.298, R.302, R.305, R.306, R.309, K.310, L.316, N.317, H.319 Ligands: DC-DG-DT-DA.2, DC-DG-DT-DA.2, DC-DG-DT-DA.2, DC-DG-DT-DA.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, 2KH.4 Protein-ligand interaction information (PLIP) not available

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

DC-DG-DT-DA.2: 22 residues within 4Å: Chain A: I.115, F.116, G.117, V.118, G.119, K.121, T.122, Q.147, H.201, D.204, F.261, R.276, D.278, W.294 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, 2KH.4, MG.5, NA.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.3: 17 residues within 4Å: Chain A: A.12, G.46, R.47, T.50, F.51, L.74, 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

1 x 2KH: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine(Non-covalent)

2KH.4: 19 residues within 4Å: Chain A: G.191, G.192, R.195, K.197, G.200, H.201, D.202, D.204, S.293, W.294, T.295, G.296, S.297, K.298, Q.301 Ligands: DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DT-DA.2, MG.5, MG.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.192, A:R.195, A:R.195, A:H.201, A:H.201, A:D.202, A:D.202, A:D.202, A:D.204, A:S.293 Water bridges: A:K.197, A:K.197, A:D.278, A:D.278, A:K.298 Salt bridges: A:K.197, A:H.201

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: D.202, D.204, D.278 Ligands: DC-DG-DT-DA.2, 2KH.4, MG.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.202, A:D.204, A:D.278, H2O.5, H2O.15 MG.6: 4 residues within 4Å: Chain A: D.202, D.204 Ligands: 2KH.4, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:D.204, H2O.6

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

NA.7: 4 residues within 4Å: Chain A: T.113, I.115, V.118 Ligands: DC-DG-DT-DA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.118, A:V.118

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

EDO.8: 5 residues within 4Å: Chain A: L.61, P.62, S.63, P.64, Q.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.63, A:S.63 EDO.9: 3 residues within 4Å: Chain A: P.18, P.348, Q.351 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.351

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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