SMTL ID : 3n9b.1 (1 other biounit)

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: H.26, D.34, H.68, I.79 Ligands: MN.6 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.36, A:R.36, A:R.36, A:Y.72 Salt bridges: A:H.26, A:H.68 SO4.2: 3 residues within 4Å: Chain A: E.119, R.161 Ligands: YT3.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.161 Salt bridges: A:R.161 SO4.3: 6 residues within 4Å: Chain A: K.120, R.161, P.162, D.163, E.168 Ligands: YT3.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.161, A:D.163 Salt bridges: A:K.120, A:R.161

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

CL.4: 1 residues within 4Å: Chain A: R.124 Ligand excluded by PLIP

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

PEG.5: 6 residues within 4Å: Chain A: P.56, K.145, D.146, G.147, A.149, R.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.149, A:R.150 Water bridges: A:R.154

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

MN.6: 4 residues within 4Å: Chain A: H.26, H.32, D.34 Ligands: SO4.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.26, A:H.32, A:D.34, H2O.3, H2O.4

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

YT3.7: 1 residues within 4Å: Chain A: D.163 No protein-ligand interaction detected (PLIP) YT3.8: 1 residues within 4Å: Chain A: E.108 No protein-ligand interaction detected (PLIP) YT3.9: 2 residues within 4Å: Chain A: E.119 Ligands: SO4.2 No protein-ligand interaction detected (PLIP) YT3.10: 3 residues within 4Å: Chain A: D.163, E.168 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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