SMTL ID : 7co6.1

Binary complex of DNA polymerase Mu with 1-nt gapped DNA (templating thymine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 27 residues within 4Å: Chain A: G.174, L.177, Q.364, H.365, F.385, E.386, R.387, K.426, Q.429, R.430, R.433, R.434, R.437, K.438, L.444, 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, GOL.4, CL.6 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: 21 residues within 4Å: Chain A: I.243, F.244, G.245, V.246, G.247, K.249, T.250, Q.275, H.329, D.330, F.389, R.404, D.406, W.422 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, K.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.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: 9 residues within 4Å: Chain A: R.387, G.421, W.422, Q.429, R.433, S.446 Ligands: DC-DG-DG-DC-DT-DT-DA-DC-DG.1, DC-DG-DT-DA.2, CL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.421, A:Q.429, A:R.433, A:R.433

1 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: T.241, I.243, V.246 Ligands: DC-DG-DT-DA.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.241, A:I.243, A:V.246, H2O.5, H2O.7

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: R.387, N.445, S.446 Ligands: DC-DG-DG-DC-DT-DT-DA-DC-DG.1, GOL.4 Ligand excluded by 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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