SMTL ID : 7cob.1

Ternary complex of DNA polymerase Mu (Q441A) with 1-nt gapped DNA (T:dGMPNPP)

Coordinates

PDB Format

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: 24 residues within 4Å: Chain A: G.174, L.177, Q.364, H.365, F.385, E.386, R.387, R.430, R.433, R.434, R.437, K.438, N.445, H.447 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, XG4.4, MG.7 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: 17 residues within 4Å: Chain A: I.243, F.244, G.245, V.246, G.247, K.249, T.250, H.329, F.389, R.404, K.426 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, XG4.4 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: 15 residues within 4Å: Chain A: A.140, 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 XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.4: 19 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, K.426, 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.2, MG.5, MG.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.320, A:R.323, A:R.323, A:H.329, A:D.330, A:K.426, A:R.433 Water bridges: A:K.325, A:K.325, A:K.325, A:K.325, A:D.406 Salt bridges: A:K.325, A:H.329

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

MG.5: 4 residues within 4Å: Chain A: D.330, D.332 Ligands: XG4.4, 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.6: 5 residues within 4Å: Chain A: D.330, D.332, D.406 Ligands: XG4.4, MG.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.330, A:D.332, A:D.406, H2O.3, H2O.9 MG.7: 1 residues within 4Å: Ligands: DC-DG-DG-DC-DT-DT-DA-DC-DG.1 No protein-ligand interaction detected (PLIP)

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