SMTL ID : 6rar.1

Pmar-Lig_PreS3-Mn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain B: C.10 Chain C: C.1 Chain D: K.163, D.165, G.166, E.216, E.315 No protein-ligand interaction detected (PLIP)

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 17 residues within 4Å: Chain C: C.1 Chain D: L.143, A.144, E.161, I.162, K.163, L.164, R.168, E.216, F.245, L.286, M.318, K.320, R.330, W.334, K.336, K.338 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.161, D:E.161, D:K.163, D:L.164, D:R.168, D:K.320, D:R.330 Salt bridges: D:K.163, D:K.336 pi-Stacking: D:F.245

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain D: H.145, D.146, N.149, H.150 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.146, D:N.149 Salt bridges: D:H.145, D:H.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williamson, A. et al., Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation. Nucleic Acids Res. (2019)

Release Date

2019-07-10

Peptides

ATP-dependent DNA ligase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
I

ATP-dependent DNA ligase

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