SMTL ID : 7co8.1

Ternary complex of DNA polymerase Mu with 2-nt gapped DNA (T:dGMPNPP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

DC-DG-DT-DA.1: 21 residues within 4Å: Chain A: F.244, G.245, V.246, G.247, K.249, T.250, Q.275, D.332, Q.366, R.387, F.389, R.404, D.406, W.422 Chain B: T.7, A.8, C.9, G.10 Ligands: XG4.3, K.4, MG.5 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.2: 15 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 Chain B: C.1, G.2, G.3, C.4 Ligands: MG.7 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)

XG4.3: 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, K.426, Q.429, R.433 Chain B: T.5, T.6 Ligands: DC-DG-DT-DA.1, 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:D.330, A:Q.429, A:R.433 Water bridges: A:K.325, A:K.325, A:K.426, A:K.426 Salt bridges: A:K.325, A:H.329

1 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: T.241, I.243, V.246 Ligands: DC-DG-DT-DA.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.241, A:I.243, A:V.246, H2O.14

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

MG.5: 6 residues within 4Å: Chain A: D.330, D.332, D.406 Ligands: DC-DG-DT-DA.1, XG4.3, MG.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.330, A:D.332, A:D.406, H2O.2 MG.6: 4 residues within 4Å: Chain A: D.330, D.332 Ligands: XG4.3, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.330, A:D.332, H2O.5 MG.7: 1 residues within 4Å: Ligands: DG-DC-DC-DG.2 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

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