SMTL ID : 5txz.1

DNA Polymerase Mu Reactant Complex, 100mM Mg2+ (15 min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: 28 residues within 4Å: Chain A: G.48, L.51, Q.238, H.239, 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, EDO.18 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: 32 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, 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, MG.5, MG.6, CA.7, NA.9, EDO.10, PPV.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: 18 residues within 4Å: Chain A: A.14, G.48, R.49, T.52, F.53, L.76, P.77, H.78, F.79, 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.18 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, MG.5, MG.6, CA.7, EDO.10, PPV.17 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.194, A:R.197, A:H.203, A:D.204 Water bridges: A:R.197, A:R.197, A:R.197, A:R.197, A:K.199, A:K.199, A:D.204 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203, A:H.203

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 7 residues within 4Å: Chain A: D.204, D.206 Ligands: DC-DG-DT-DA-DT.2, TTP.4, MG.6, CA.7, PPV.17 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.4 MG.6: 8 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, MG.5, CA.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.15

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 8 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, MG.5, 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.15

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.8: 1 residues within 4Å: Chain A: C.54 No protein-ligand interaction detected (PLIP)

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

NA.9: 4 residues within 4Å: Chain A: T.115, I.117, V.120 Ligands: DC-DG-DT-DA-DT.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.115, A:V.120

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

EDO.10: 8 residues within 4Å: Chain A: R.261, G.295, W.296, R.307, S.320 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:R.307, A:S.320 Water bridges: A:R.307 EDO.11: 3 residues within 4Å: Chain A: T.188, T.210, F.289 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.190 EDO.12: 3 residues within 4Å: Chain A: W.317, F.324, F.331 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.319, A:N.319 EDO.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.14: 1 residues within 4Å: Chain A: G.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.216 EDO.15: 4 residues within 4Å: Chain A: G.45, S.46, E.47, G.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.45, A:E.47, A:G.48 EDO.18: 4 residues within 4Å: 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, DG-DC-DC-DG.3 No protein-ligand interaction detected (PLIP)

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

EPE.16: 4 residues within 4Å: Chain A: L.23, K.199, L.200, Q.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.200, A:Q.201

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.17: 11 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, MG.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.194, A:H.203, A:D.204 Water bridges: A:R.197, A:R.197, A:R.197, A:R.197, A:K.199, A:K.199 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