SMTL ID : 3n9d.1

Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.26, H.32, D.34 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.26, A:H.32, A:D.34

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

SO4.2: 4 residues within 4Å: Chain A: H.26, D.34, H.68 Ligands: MN.1 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.26, A:R.36, A:R.36 Salt bridges: A:H.26, A:H.68 SO4.3: 3 residues within 4Å: Chain A: E.119, R.161 Ligands: YT3.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.161, A:R.161 Salt bridges: A:R.161

2 x YT3: YTTRIUM (III) ION(Non-covalent)

YT3.4: 2 residues within 4Å: Chain A: E.105, E.108 No protein-ligand interaction detected (PLIP) YT3.5: 2 residues within 4Å: Chain A: E.119 Ligands: SO4.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nair, P.A. et al., Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-08-11

Peptides

Probable ATP-dependent DNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable ATP-dependent DNA ligase

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