SMTL ID : 4m04.1

Human DNA Polymerase Mu ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x DC- DG- DG- DC- DA- DT- DA- DC- DG: template strand(Non-covalent)

DC-DG-DG-DC-DA-DT-DA-DC-DG.1: 25 residues within 4Å: Chain A: G.48, L.51, Q.238, F.259, E.260, R.261, F.263, K.300, R.304, R.307, R.308, R.311, K.312, L.318, N.319, H.321 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, DUP.4 Protein-ligand interaction information (PLIP) not available

1 x DC- DG- DT- DA: upstream primer strand(Non-covalent)

DC-DG-DT-DA.2: 24 residues within 4Å: Chain A: I.117, F.118, G.119, V.120, G.121, K.123, T.124, Q.149, H.203, D.206, R.261, F.263, R.278, D.280, W.296 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, DUP.4, MG.5, EDO.8, NA.10 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: downstream primer strand(Non-covalent)

DG-DC-DC-DG.3: 17 residues within 4Å: Chain A: A.14, G.48, R.49, T.52, F.53, R.55, P.77, H.78, G.80, E.81, H.82, S.83 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, EDO.7 Protein-ligand interaction information (PLIP) not available

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.4: 19 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, G.202, H.203, D.204, D.206, G.295, W.296, T.297, G.298, S.299, K.300 Ligands: DC-DG-DG-DC-DA-DT-DA-DC-DG.1, DC-DG-DT-DA.2, MG.5, MG.6, EDO.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.300 Hydrogen bonds: A:G.194, A:R.197, A:R.197, A:H.203, A:H.203, A:D.204, A:D.204 Water bridges: A:K.199, A:K.199, A:H.203, A:K.300 Salt bridges: A:K.199, A:H.203

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: DC-DG-DT-DA.2, DUP.4, MG.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.1 MG.6: 4 residues within 4Å: Chain A: D.204, D.206 Ligands: DUP.4, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.1

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

EDO.7: 4 residues within 4Å: Chain A: E.81, H.82, R.85 Ligands: DG-DC-DC-DG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.85 Water bridges: A:H.82 EDO.8: 6 residues within 4Å: Chain A: R.261, G.295, W.296, R.307 Ligands: DC-DG-DT-DA.2, DUP.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.295, A:R.307, A:R.307 EDO.11: 3 residues within 4Å: Chain A: Q.288, H.321, F.331 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.288, A:H.321

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

CL.9: 4 residues within 4Å: Chain A: S.46, E.47, G.48, R.49 Ligand excluded by PLIP

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

NA.10: 4 residues within 4Å: Chain A: T.115, I.117, V.120 Ligands: DC-DG-DT-DA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.120, A:V.120

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 4 residues within 4Å: Chain A: L.23, K.199, L.200, Q.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.200, A:Q.201 Salt bridges: A:K.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, A.F. et al., Sustained active site rigidity during synthesis by human DNA polymerase mu. Nat.Struct.Mol.Biol. (2014)

Release Date

2014-02-05

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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