SMTL ID : 7cod.1

Post insertion complex of DNA polymerase Mu (K438A/Q441A) with 1-nt gapped DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

DC-DG-DG-DC-DT-DT-DA-DC-DG.1: 22 residues within 4Å: Chain A: G.174, L.177, Q.364, H.365, F.385, E.386, R.387, R.430, R.433, K.438, N.445, H.447 Ligands: DC-DG-DT-DA-DG.2, DC-DG-DT-DA-DG.2, DC-DG-DT-DA-DG.2, DC-DG-DT-DA-DG.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, GOL.4, DGT.5 Protein-ligand interaction information (PLIP) not available

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

DC-DG-DT-DA-DG.2: 23 residues within 4Å: Chain A: E.165, K.238, T.241, Q.242, I.243, F.244, G.245, V.246, G.247, V.248, K.249, T.250, H.329, F.389, R.404 Ligands: DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1, GOL.4, DGT.5, NA.8 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.174, R.175, T.178, F.179, P.203, H.204, G.206, E.207, H.208, S.209 Ligands: DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1 Protein-ligand interaction information (PLIP) not available

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: R.387, G.421, W.422, S.446 Ligands: DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DG.2, DGT.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.446, A:S.446 Water bridges: A:R.433, A:R.433, A:S.446

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.5: 20 residues within 4Å: Chain A: G.319, G.320, R.323, K.325, G.328, H.329, D.330, D.332, G.421, W.422, T.423, G.424, R.433 Ligands: DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DG.2, DC-DG-DT-DA-DG.2, GOL.4, MG.6, MG.7 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.320, A:H.329, A:D.330, A:D.330, A:W.422, A:R.433 Water bridges: A:R.323, A:R.323, A:R.323, A:D.406, A:D.406, A:R.433, A:R.433 Salt bridges: A:R.323, A:K.325, A:K.325, A:H.329, A:H.329

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

MG.6: 5 residues within 4Å: Chain A: D.330, D.332, D.406 Ligands: DGT.5, MG.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.330, A:D.332, A:D.406, H2O.2, H2O.3 MG.7: 4 residues within 4Å: Chain A: D.330, D.332 Ligands: DGT.5, MG.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.330, A:D.332, H2O.4 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.8: 5 residues within 4Å: Chain A: T.241, I.243, V.246 Ligands: DC-DG-DT-DA-DG.2, DC-DG-DT-DA-DG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.241, A:V.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, M. et al., Mechanism of genome instability mediated by human DNA polymerase mu misincorporation. Nat Commun (2021)

Release Date

2021-06-30

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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