SMTL ID : 6p0b.1

Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

DG-DT-DC-DG-DG-DA-DC.1: 29 residues within 4Å: Chain A: S.44, A.45, R.46, K.309, R.330, K.485, K.487, Y.490, K.511, T.539, G.540, F.541, S.542, D.543, E.544, F.613, R.615 Chain B: C.11 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7, G.8 Ligands: MG.2, MG.3, AMP.7 44 PLIP interactions: 44 interactions with chain A Hydrogen bonds: A:R.46, A:R.46, A:L.193, A:G.194, A:L.195, A:A.196, A:Q.198, A:S.199, A:S.199, A:R.298, A:Q.377, A:T.380, A:R.509, A:K.511, A:K.511, A:K.536, A:S.591, A:S.593, A:S.593, A:Y.596 Water bridges: A:R.190, A:R.192, A:R.192, A:H.287, A:R.298, A:R.384, A:S.480, A:R.512, A:R.512, A:R.512, A:R.512, A:G.517, A:K.536, A:K.536, A:G.538, A:T.539, A:F.613 Salt bridges: A:R.190, A:K.245, A:H.287, A:R.479, A:K.511, A:K.536, A:K.536

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

MG.2: 7 residues within 4Å: Chain A: K.309, D.311, G.312, E.461 Chain B: C.11 Ligands: DG-DT-DC-DG-DG-DA-DC.1, AMP.7 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: G.540 Ligands: DG-DT-DC-DG-DG-DA-DC.1, DG-DT-DC-DG-DG-DA-DC.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.540, H2O.3, H2O.4, H2O.7, H2O.13 MG.4: 1 residues within 4Å: Chain A: D.574 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: T.6, G.7 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain A: M.221, A.224, K.228, W.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.228

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.7: 16 residues within 4Å: Chain A: A.286, E.307, Y.308, K.309, Y.310, R.314, R.330, E.362, F.401, A.437, M.464, K.466, W.483, K.485 Ligands: DG-DT-DC-DG-DG-DA-DC.1, MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.307, A:E.307, A:K.309, A:Y.310, A:R.314, A:R.330, A:K.466 Water bridges: A:R.330, A:K.485 Salt bridges: A:K.309, A:K.485 pi-Stacking: A:F.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tumbale, P.P. et al., Two-tiered enforcement of high-fidelity DNA ligation. Nat Commun (2019)

Release Date

2019-12-11

Peptides

DNA ligase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase 1

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