SMTL ID : 5tyv.1

DNA Polymerase Mu Reactant Complex, Mn2+ (7.5 min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

DC-DG-DG-DC-DA-DT-DA-DC-DG.1: 27 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-DT.2, DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, TTP.4, MN.15 Protein-ligand interaction information (PLIP) not available

1 x DC- DG- DT- DA- DT: DNA (5'-D(*CP*GP*TP*AP*T)-3')(Non-covalent)

DC-DG-DT-DA-DT.2: 33 residues within 4Å: Chain A: I.117, F.118, G.119, V.120, G.121, K.123, T.124, Q.149, R.197, H.203, D.204, D.206, F.263, R.278, D.280, 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-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, TTP.4, MN.5, MN.6, NA.10, PPV.14, MN.16, EDO.17 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: 16 residues within 4Å: Chain A: A.14, G.48, R.49, T.52, F.53, 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, MN.9 Protein-ligand interaction information (PLIP) not available

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.4: 22 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-DT.2, DC-DG-DT-DA-DT.2, MN.5, MN.6, PPV.14, MN.16, EDO.17 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:K.300 Hydrogen bonds: A:G.194, A:R.197, A:H.203 Water bridges: A:R.197, A:R.197, A:R.197, A:R.197, A:K.199, A:K.199, A:H.203, A:H.203, A:H.203, A:D.204, A:D.204, A:D.204 Salt bridges: A:R.197, A:K.199, A:H.203, A:H.203

7 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.5: 6 residues within 4Å: Chain A: D.204, D.206 Ligands: DC-DG-DT-DA-DT.2, TTP.4, MN.6, PPV.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.3 MN.6: 7 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, TTP.4, MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.12 MN.7: 2 residues within 4Å: Chain A: E.260, H.321 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.260, A:H.321, H2O.8, H2O.10, H2O.11 MN.8: 2 residues within 4Å: Chain A: E.92, H.93 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.92, A:H.93 MN.9: 2 residues within 4Å: Chain A: H.82 Ligands: DG-DC-DC-DG.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.82, H2O.9, H2O.14 MN.15: 1 residues within 4Å: Ligands: DC-DG-DG-DC-DA-DT-DA-DC-DG.1 No protein-ligand interaction detected (PLIP) MN.16: 4 residues within 4Å: Chain A: H.203 Ligands: DC-DG-DT-DA-DT.2, TTP.4, PPV.14 No protein-ligand interaction detected (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-DT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.115, A:G.119, A:V.120

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

EDO.11: 4 residues within 4Å: Chain A: P.64, S.65, P.66, Q.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.65, A:S.65 EDO.12: 3 residues within 4Å: Chain A: C.54, K.300, R.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.304, A:R.304 EDO.17: 7 residues within 4Å: Chain A: R.261, G.295, W.296, R.307 Ligands: DC-DG-DT-DA-DT.2, DC-DG-DT-DA-DT.2, TTP.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.261, A:R.261, A:G.295, A:R.307, A:R.307

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

EPE.13: 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

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.14: 12 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, G.202, H.203, D.204, D.206 Ligands: DC-DG-DT-DA-DT.2, TTP.4, MN.5, MN.16 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.194, A:H.203 Water bridges: A:R.197, A:R.197, A:K.199, A:K.199, A:K.199, A:H.203, A:H.203 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamsen, J.A. et al., Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Nat Commun (2017)

Release Date

2017-08-30

Peptides

DNA-directed DNA/RNA polymerase mu: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA/RNA polymerase mu

Related Entries With Identical Sequence