SMTL ID : 5vzi.1

Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming dTTP

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: 27 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-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, TTP.5 Protein-ligand interaction information (PLIP) not available

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

DC-DG-DT-DA-DT.2: 33 residues within 4Å: Chain A: I.115, F.116, G.117, V.118, G.119, K.121, T.122, Q.147, G.191, R.195, H.201, D.202, D.204, F.261, R.276, D.278, G.293, H.294, T.295, G.296, K.298 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, TTP.4, TTP.5, MG.6, MG.7, NA.8, NA.9, MG.15 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: 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 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

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.4: 11 residues within 4Å: Chain A: G.191, G.192, R.195, K.197, H.201, D.202, D.204 Ligands: DC-DG-DT-DA-DT.2, TTP.5, MG.6, MG.15 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.192 Water bridges: A:R.195, A:R.195, A:R.195, A:R.195, A:K.197 Salt bridges: A:R.195, A:K.197, A:K.197, A:H.201 TTP.5: 22 residues within 4Å: Chain A: G.191, G.192, R.195, K.197, G.200, H.201, D.202, D.204, G.293, H.294, T.295, G.296, S.297, K.298 Ligands: DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, TTP.4, MG.6, MG.7, NA.9, MG.15 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.192, A:R.195, A:H.201, A:D.202, A:K.298 Water bridges: A:R.195, A:R.195, A:R.195, A:R.195, A:K.197, A:K.197, A:D.278, A:R.305 Salt bridges: A:R.195, A:K.197, A:K.197, A:H.201, A:H.201

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.6: 7 residues within 4Å: Chain A: D.202, D.204 Ligands: DC-DG-DT-DA-DT.2, TTP.4, TTP.5, MG.7, NA.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:D.204, H2O.4 MG.7: 8 residues within 4Å: Chain A: D.202, D.204, D.278 Ligands: DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, TTP.5, MG.6, NA.9 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.16 MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain A: H.201 Ligands: DC-DG-DT-DA-DT.2, TTP.4, TTP.5 No protein-ligand interaction detected (PLIP)

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

NA.8: 4 residues within 4Å: Chain A: T.113, I.115, V.118 Ligands: DC-DG-DT-DA-DT.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.113, A:V.118 NA.9: 8 residues within 4Å: Chain A: D.202, D.204, D.278 Ligands: DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, TTP.5, MG.6, MG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.204, A:D.278

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

EDO.10: 3 residues within 4Å: Chain A: W.315, F.322, F.329 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.317 EDO.11: 5 residues within 4Å: Chain A: T.160, P.161, L.163, Q.268, K.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.268, A:Q.268, A:K.273 EDO.12: 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 EDO.13: 9 residues within 4Å: Chain A: E.258, R.259, V.280, V.281, A.282, A.290, H.294, S.318, H.319 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.259, A:V.281, A:S.318, A:S.318 Water bridges: A:H.319

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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