SMTL ID : 4yd1.1

Ternary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate and an incoming nonhydrolyzable dUMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: 23 residues within 4Å: Chain A: F.116, G.117, V.118, G.119, K.121, T.122, Q.147, D.204, Q.238, R.259, F.261, R.276, D.278, W.294 Chain B: A.6, T.7, A.8, C.9, G.10 Ligands: MG.3, EDO.8, DUP.9, NA.14 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: 14 residues within 4Å: Chain A: G.46, R.47, T.50, F.51, P.75, H.76, G.78, E.79, H.80, S.81 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

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

MG.3: 6 residues within 4Å: Chain A: D.202, D.204, D.278 Ligands: DC-DG-DT-DA.1, MG.4, DUP.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:D.204, A:D.278, H2O.3 MG.4: 4 residues within 4Å: Chain A: D.202, D.204 Ligands: MG.3, DUP.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:D.204, H2O.6 MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.5: 5 residues within 4Å: Chain A: L.61, P.62, S.63, P.64, Q.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.63 Water bridges: A:S.63, A:S.63 EDO.8: 6 residues within 4Å: Chain A: G.293, W.294, R.305, S.318 Ligands: DC-DG-DT-DA.1, DUP.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.293, A:R.305, A:R.305, A:S.318

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: W.315, F.322, F.329 Chain B: T.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.317 Water bridges: A:N.317 GOL.7: 1 residues within 4Å: Chain A: Q.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.228

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

DUP.9: 19 residues within 4Å: Chain A: G.191, G.192, R.195, K.197, G.200, H.201, D.202, D.204, G.293, W.294, T.295, G.296, K.298, Q.301 Chain B: A.5 Ligands: DC-DG-DT-DA.1, MG.3, MG.4, EDO.8 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.192, A:R.195, A:R.195, A:H.201, A:D.202 Water bridges: A:K.197, A:K.197, A:H.201, A:H.201, A:D.202, A:D.202, A:K.298 Salt bridges: A:K.197, A:H.201

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

CL.10: 4 residues within 4Å: Chain A: S.44, E.45, G.46, R.47 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: L.291, S.334, E.335 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: K.197, L.198, Q.199 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: F.257, R.259, W.294 Ligand excluded by PLIP

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

NA.14: 4 residues within 4Å: Chain A: T.113, I.115, V.118 Ligands: DC-DG-DT-DA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.113, A:V.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, A.F. et al., Creative template-dependent synthesis by human polymerase mu. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-08-05

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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